Francis Xavier was born in the royal castle of Xavier, in the Kingdom of Navarre, on 7 April 1506 according to a family register. He was the youngest son of Juan de Jasso y Atondo, seneschal of Xavier castle, who belonged to a prosperous farming family and had acquired a doctorate in law at the University of Bologna, and later became privy counsellor and Finance minister to King John III of Navarre (Jean d'Albret). Francis's mother was Doña María de Azpilcueta y Aznárez, sole heiress of two noble Navarrese families. He was thus related to the great theologian and Philosopher Martín de Azpilcueta.

In 1512, Ferdinand, King of Aragon and regent of Castile, invaded Navarre, initiating a war that lasted over 18 years. Three years later, Francis's father died when Francis was only nine years old. In 1516, Francis's brothers participated in a failed Navarrese-French attempt to expel the Spanish invaders from the kingdom. The Spanish Governor, Cardinal Cisneros, confiscated the family lands, demolished the outer wall, the gates, and two towers of the family castle, and filled in the moat. In addition, the height of the keep was reduced by half. Only the family residence inside the castle was left. In 1522 one of Francis's brothers participated with 200 Navarrese nobles in dogged but failed resistance against the Castilian Count of Miranda in Amaiur, Baztan, the last Navarrese territorial position south of the Pyrenees.

In 1525, Francis went to study in Paris at the Collège Sainte-Barbe, University of Paris, where he would spend the next eleven years. In the early days he acquired some reputation as an athlete and a high-jumper.

In 1529, Francis shared lodgings with his friend Pierre Favre. A new student, Ignatius of Loyola, came to room with them. At 38, Ignatius was much older than Pierre and Francis, who were both 23 at the time. Ignatius convinced Pierre to become a priest, but was unable convince Francis, who had aspirations of worldly advancement. At first Francis regarded the new lodger as a joke and was sarcastic about his efforts to convert students. When Pierre left their lodgings to visit his family and Ignatius was alone with Francis, he was able to slowly break down Francis's resistance. According to most biographies Ignatius is said to have posed the question: "What will it profit a man to gain the whole world, and lose his own soul?" However, according to James Broderick such method is not characteristic of Ignatius and there is no evidence that he employed it at all.

In 1530 Francis received the degree of Master of Arts, and afterwards taught Aristotelian philosophy at Beauvais College, University of Paris.

On 15 August 1534, seven students met in a crypt beneath the Church of Saint Denis (now Saint Pierre de Montmartre), in Montmartre outside Paris. They were Francis, Ignatius of Loyola, Alfonso Salmeron, Diego Laínez, Nicolás Bobadilla from Spain, Peter Faber from Savoy, and Simão Rodrigues from Portugal. They made private vows of poverty, chastity, and obedience to the Pope, and also vowed to go to the Holy Land to convert infidels. Francis began his study of theology in 1534 and was ordained on 24 June 1537.

In 1539, after long discussions, Ignatius drew up a formula for a new religious order, the Society of Jesus (the Jesuits). Ignatius's plan for the order was approved by Pope Paul III in 1540.

Leaving Rome on 15 March 1540, in the Ambassador's train, Francis took with him a breviary, a catechism, and De Institutione bene vivendi by Croatian humanist Marko Marulić, a Latin book that had become popular in the Counter-Reformation. According to a 1549 letter of F. Balthasar Gago in Goa, it was the only book that Francis read or studied. Francis reached Lisbon in June 1540 and four days after his arrival, he and Rodrigues were summoned to a private audience with the King and the Queen.

Francis Xavier left Lisbon on 7 April 1541, his thirty-fifth birthday, along with two other Jesuits and the new viceroy Martim Afonso de Sousa, on board the Santiago. As he departed, Francis was given a brief from the pope appointing him apostolic nuncio to the East. From August until March 1542 he remained in Portuguese Mozambique, and arrived in Goa, then capital of Portuguese India on 6 May 1542, thirteen months after leaving Lisbon.

Xavier soon learned that along the Pearl Fishery Coast, which extends from Cape Comorin on the southern tip of India to the island of Mannar, off Ceylon (Sri Lanka), there was a Jāti of people called Paravas. Many of them had been baptised ten years before, merely to please the Portuguese, who had helped them against the Moors, but remained uninstructed in the faith. Accompanied by several native clerics from the seminary at Goa, he set sail for Cape Comorin in October 1542. He taught those who had already been baptised, and preached to those who weren't. His efforts with the high-caste Brahmins remained unavailing.

Europeans had already come to Japan: the Portuguese had landed in 1543 on the island of Tanegashima, where they introduced the first firearms to Japan.

He devoted almost three years to the work of preaching to the people of southern India and Ceylon, converting many. He built nearly 40 churches along the coast, including St. Stephen's Church, Kombuthurai, mentioned in his letters dated 1544.

In the spring of 1545 Xavier started for Portuguese Malacca. He laboured there for the last months of that year. About January 1546, Xavier left Malacca for the Maluku Islands, where the Portuguese had some settlements. For a year and a half he preached the Gospel there. He went first to Ambon Island, where he stayed until mid-June. He then visited other Maluku Islands, including Ternate, Baranura, and Morotai. Shortly after Easter 1547, he returned to Ambon Island; a few months later he returned to Malacca.

The role of Francis Xavier in the Goa Inquisition is controversial. He had written to King João III of Portugal in 1546, encouraging him to dispatch the Inquisition to Goa, which he did many years later in 1560. Francis Xavier died in 1552 without living to see the horrors of the Goa Inquisition, but some historians believe that he was aware of the Portuguese Inquisition's brutality. In an interview to an Indian newspaper, Historian Teotónio de Souza stated that Francis Xavier and Simão Rodrigues, another founder-member of the Society of Jesus, were together in Lisbon before Francis left for India. Both were asked to assist spiritually the prisoners of the Inquisition and were present at the very first auto-da-fé celebrated in Portugal in September 1540, at which 23 were absolved and two were condemned to be burnt, including a French cleric. Hence, he believes that Xavier was aware of the brutality of the Inquisition.

In Malacca in December 1547, Francis Xavier met a Japanese man named Anjirō. Anjirō had heard of Francis in 1545 and had travelled from Kagoshima to Malacca to meet him. Having been charged with murder, Anjirō had fled Japan. He told Francis extensively about his former life and the customs and culture of his homeland. Anjirō became the first Japanese Christian and adopted the name of 'Paulo de Santa Fe'. He later helped Xavier as a mediator and interpreter for the mission to Japan that now seemed much more possible.

From Amboina, he wrote to his companions in Europe: "I asked a Portuguese merchant, … who had been for many days in Anjirō’s country of Japan, to give me … some information on that land and its people from what he had seen and heard …. All the Portuguese merchants coming from Japan tell me that if I go there I shall do great Service for God our Lord, more than with the pagans of India, for they are a very reasonable people. (To His Companions Residing in Rome, From Cochin, 20 January 1548, no. 18, p. 178).

Francis Xavier reached Japan on 27 July 1549, with Anjiro and three other Jesuits, but he was not permitted to enter any port his ship arrived at until 15 August, when he went ashore at Kagoshima, the principal port of Satsuma Province on the island of Kyūshū. As a representative of the Portuguese king, he was received in a friendly manner. Shimazu Takahisa (1514–1571), daimyō of Satsuma, gave a friendly reception to Francis on 29 September 1549, but in the following year he forbade the conversion of his subjects to Christianity under penalty of death; Christians in Kagoshima could not be given any catechism in the following years. The Portuguese missionary Pedro de Alcáçova would later write in 1554:

He was hosted by Anjirō's family until October 1550. From October to December 1550, he resided in Yamaguchi. Shortly before Christmas, he left for Kyoto but failed to meet with the Emperor. He returned to Yamaguchi in March 1551, where he was permitted to preach by the daimyo of the province. However, lacking fluency in the Japanese language, he had to limit himself to reading aloud the translation of a catechism.

With the passage of time, his sojourn in Japan could be considered somewhat fruitful as attested by congregations established in Hirado, Yamaguchi, and Bungo. Xavier worked for more than two years in Japan and saw his successor-Jesuits established. He then decided to return to India. Historians debate the exact path he returned by, but from evidence attributed to the captain of his ship, he may have travelled through Tanegeshima and Minato, and avoided Kagoshima because of the hostility of the daimyo. During his trip, a tempest forced him to stop on an island near Guangzhou, China where he met Diogo Pereira, a rich merchant and an old friend from Cochin. Pereira showed him a letter from Portuguese prisoners in Guangzhou, asking for a Portuguese ambassador to speak to the Chinese Emperor on their behalf. Later during the voyage, he stopped at Malacca on 27 December 1551, and was back in Goa by January 1552.

In late August 1552, the Santa Cruz reached the Chinese island of Shangchuan, 14 km away from the southern coast of mainland China, near Taishan, Guangdong, 200 km south-west of what later became Hong Kong. At this time, he was accompanied only by a Jesuit student, Álvaro Ferreira, a Chinese man called António, and a Malabar servant called Christopher. Around mid-November he sent a letter saying that a man had agreed to take him to the mainland in exchange for a large sum of money. Having sent back Álvaro Ferreira, he remained alone with António. He died at Shangchuan, Taishan, China from a fever on 3 December 1552, while he was waiting for a boat that would take him to mainland China.

He was first buried on a beach at Shangchuan Island, Taishan, Guangdong. His incorrupt body was taken from the island in February 1553 and was temporarily buried in St. Paul's church in Portuguese Malacca on 22 March 1553. An open grave in the church now marks the place of Xavier's burial. Pereira came back from Goa, removed the corpse shortly after 15 April 1553, and moved it to his house. On 11 December 1553, Xavier's body was shipped to Goa. The body is now in the Basilica of Bom Jesus in Goa, where it was placed in a glass container encased in a silver casket on 2 December 1637. This casket, constructed by Goan silversmiths between 1636 and 1637, was an exemplary blend of Italian and Indian aesthetic sensibilities. There are 32 silver plates on all the four sides of the casket depicting different episodes from the life of the Saint:

The right forearm, which Xavier used to bless and baptise his converts, was detached by Superior General Claudio Acquaviva in 1614. It has been displayed since in a silver reliquary at the main Jesuit church in Rome, Il Gesù.

Francis Xavier was beatified by Paul V on 25 October 1619, and was canonized by Gregory XV on 12 March (12 April) 1622, at the same time as Ignatius Loyola. Pius XI proclaimed him the "Patron of Catholic Missions". His feast day is 3 December.

The Novena of Grace is a popular devotion to Francis Xavier, typically prayed either on the nine days before 3 December, or on 4 March through 12 March (the anniversary of Pope Gregory XV's canonisation of Xavier in 1622). It began with the Italian Jesuit missionary Marcello Mastrilli. Before he could travel to the Far East, Mastrilli was gravely injured in a freak accident after a festive celebration dedicated to the Immaculate Conception in Naples. Delirious and on the verge of death, Mastrilli saw Xavier, who he later said asked him to choose between travelling or death by holding the respective symbols, to which Mastrilli answered, "I choose that which God wills." Upon regaining his health, Mastrilli made his way via Goa and the Philippines to Satsuma, Japan. The Tokugawa shogunate beheaded the missionary in October 1637, after undergoing three days of tortures involving the volcanic sulphurous fumes from Mt. Unzen, known as the Hell mouth or "pit" that had supposedly caused an earlier missionary to renounce his faith.

Many churches all over the world, often founded by Jesuits, have been named in honour of Xavier. Those in the United States include the historic St. Francis Xavier Shrine at Warwick, Maryland, (founded 1720, and at which American founding father, Charles Carroll of Carrollton, (1737–1832), (longest living signer and only Catholic at the Continental Congress to sign the Declaration of Independence, 1776) and cousin to the first American-born Bishop John Carroll, (1735–1815), Bishop and later Archbishop of Baltimore, 1790–1815, (at the Roman Catholic Archdiocese of Baltimore) began their education), also the American educational teaching order Xaverian Brothers, the Basilica of St. Francis Xavier in Dyersville, Iowa, and the Mission San Xavier del Bac in Tucson, Arizona (founded in 1692, and known for its Spanish Colonial architecture).

Francis Xavier is the patron saint of his native Navarre, which celebrates his feast day on 3 December as a government holiday. In addition to Roman Catholic masses remembering Xavier on that day (now known as the Day of Navarra), celebrations in the surrounding weeks honour the region's cultural heritage. Furthermore, in the 1940s, devoted Catholics instituted the Javierada, an annual day-long pilgrimage (often on foot) from the capital at Pamplona to Xavier, where his order has built a basilica and museum and restored his family's castle.

Another of Xavier's arm bones was brought to Macau where it was kept in a silver reliquary. The relic was destined for Japan but religious persecution there persuaded the church to keep it in Macau's Cathedral of St. Paul. It was subsequently moved to St. Joseph's and in 1978 to the Chapel of St. Francis Xavier on Coloane Island. More recently the relic was moved to St. Joseph's Church.

As the foremost saint from Navarre and one of the main Jesuit saints, he is much venerated in Spain and the Hispanic countries where Francisco Javier or Javier are Common male given names. The alternative spelling Xavier is also popular in Portugal, Catalonia, Brazil, France, Belgium, and southern Italy. In India, the spelling Xavier is almost always used, and the name is quite Common among Christians, especially in Goa and the southern states of Tamil Nadu, Kerala, and Karnataka. The names Francisco Xavier, António Xavier, João Xavier, Caetano Xavier, Domingos Xavier et cetera, were very Common till quite recently in Goa. Fransiskus Xaverius is commonly used as a name for Indonesian Catholics, usually abbreviated as FX. In Austria and Bavaria the name is spelled as Xaver (pronounced (ˈk͡saːfɐ)) and often used in addition to Francis as Franz-Xaver (frant͡sˈk͡saːfɐ). Many Catalan men are named for him, often using the two-name combination Francesc Xavier. In English speaking countries, "Xavier" until recently was likely to follow "Francis"; in the 2000s, however, "Xavier" by itself has become more popular than "Francis", and since 2001 is now one of the hundred most Common male baby names in the U.S.A. Furthermore, the Sevier family name, possibly most famous in the United States for John Sevier originated from the name Xavier.

In 2006, on the 500th anniversary of his birth, the Xavier Tomb Monument and Chapel on the Shangchuan Island, in ruins after years of neglect under communist rule in China was restored with the support from the alumni of Wah Yan College, a Jesuit high school in Hong Kong.

Saint Francis Xavier is noteworthy for his missionary work, both as organiser and as pioneer, reputed to have converted more people than anyone else has done since Saint Paul. Pope Benedict XVI said of both Ignatius of Loyola and Francis Xavier: "not only their history which was interwoven for many years from Paris and Rome, but a unique Desire — a unique passion, it could be said — moved and sustained them through different human events: the passion to give to God-Trinity a glory always greater and to work for the proclamation of the Gospel of Christ to the peoples who had been ignored." By consulting with the earlier ancient Christians of St. Thomas in India, Xavier developed Jesuit missionary methods. His success also spurred many Europeans to join the order, as well as become missionaries throughout the world. His personal efforts most affected Christians in India and the East Indies (Indonesia, Malaysia, Timor). India still has numerous Jesuit missions, and many more schools. Xavier also worked to propagate Christianity in China and Japan. However, following the persecutions of Toyotomi Hideyoshi and the subsequent closing of Japan to foreigners, the Christians of Japan were forced to go underground to develop an independent Christian culture. Likewise, while Xavier inspired many missionaries to China, Chinese Christians also were forced underground and developed their own Christian culture.

Saint Francis Xavier is a major venerated saint in both Sonora and the neighbouring U.S. state of Arizona. In Magdalena de Kino in Sonora, Mexico in the Church of Santa María Magdalena, there is reclining statue of San Francisco Xavier brought by pioneer Jesuit missionary Padre Eusebio Kino in the early 18th century. The statue is said to be miraculous and is the object of pilgrimage for many of the region. Also Mission San Xavier del Bac is a pilgrimage site. The mission is an active parish church ministering to the people of the San Xavier District, Tohono O'odham Nation and nearby Tucson, Arizona.