Margaret of Valois was born on May 14, 1553, at the royal Château de Saint-Germain-en-Laye, the seventh child and third daughter of Henry II and Catherine de' Medici. Three of her brothers would become kings of France: Francis II, Charles IX and Henry III. Her sister, Elisabeth of Valois, would become the third wife of King Philip II of Spain.

Traditionally believed to have been instigated by Catherine de' Medici, the marriage was an occasion on which many of the most wealthy and prominent Huguenots had gathered in largely-Catholic Paris. That took place during the period 1562 to 1598, known as the French Wars of Religion, with factional disputes between the aristocratic houses of France, such as the House of Bourbon and the House of Guise (Lorraine). Henry of Navarre had to feign conversion to Catholicism.

At the French court, she studied grammar, classics, history and Holy Scripture. Margaret learned to speak Italian, Spanish, Latin and Greek in addition to her native French. She was competent also in prose, poetry, horsemanship and dance. She traveled with her family and the court in the grand tour of France (1564-1566). During this period Margaret had direct experience of the dangerous and complex political situation in France, and learned from her mother the art of political mediation.

In 1565, Catherine met with Philip II's chief minister the Duke of Alba at Bayonne in hopes of arranging a marriage between Margaret and Carlos, Prince of Asturias. However, Alba refused any consideration of a dynastic marriage. Other marriage negotiations with Sebastian of Portugal and Archduke Rudolf also did not succeed.

During her teenage years, she and her brother Henry were very close friends. In 1568, leaving court to command the royal armies, he entrusted his 15-year-old sister with the defense of his interests with their mother.

By 1570, Catherine de' Medici was seeking a marriage between Margaret and Henry of Navarra, a Huguenot (French Calvinist Protestant). It was hoped this union would reunite family ties, as the Bourbons were part of the French Royal family and the closest relatives to the reigning Valois branch, and create harmony between Catholics and Huguenots.

The marriage of the 19-year-old Margaret to Henry, who had become King of Navarre upon the death of his mother, Jeanne d'Albret, took place on 18 August 1572 at Notre Dame cathedral in Paris. The marriage between a Roman Catholic and a Huguenot was controversial. Pope Gregory XIII refused to grant a dispensation for the wedding, and the different faiths of the bridal couple made for an unusual wedding Service. The King of Navarre had to remain outside the cathedral during the mass, where his place was taken by Duke of Anjou.

In 1573, Charles IX's fragile mental state and constitution deteriorated further, but the heir presumptive, his brother Henry, was elected king of Poland. Due to Henry's support of suppressing Protestant worship, moderate Catholic lords, called Malcontents, supported a plot to raise Charles' youngest brother, Francis of Alençon, to the throne of France instead. Alençon appeared willing to compromise in religious affairs, making him an appealing option to those tired of violence. Allied with the Protestants, the Malcontents executed several plots to seize power.

In April 1574 the conspiracy was exposed, the Leaders of the plot were arrested and decapitated, including Joseph Boniface de La Mole, pretended lover of Margaret. After the failure of the conspiracy, Francis and Henry were held as prisoners at the Château de Vincennes. Margaret wrote a letter pleading for her husband, the Supporting Statement for Henry of Bourbon. She recorded in her Memoirs:

Alençon and Navarre finally managed to escape, one in September 1575 and the other in 1576. Henry did not even warn his wife of his departure. Margaret found herself confined to her chambers in the Louvre, under suspicion as her husband's accomplice. She wrote in her Memoirs:

In 1577, Margaret asked permission to go on a mission in the south of the Netherlands on behalf of her younger brother Francis d'Alençon. The Flemings, who had rebelled against Spanish rule in 1576, seemed willing to offer a throne to a foreign Prince who was tolerant and willing to provide them with the diplomatic and military forces necessary to protect their independence. Henry III accepted the proposal of his sister because he would finally release the inconvenient duke of Alençon.

After reporting her mission to her younger brother, Margaret returned to the court. The fighting multiplied between Henry III's mignons and Alençon's supporters, in the forefront of which Bussy d'Amboise, a lover of Margaret. In 1578 Alençon asked to be absent. But Henry III saw in it the proof of his participation in a conspiracy: he had him arrested in the middle of the night, and kept him in his room, where Margaret joined him. As for Bussy, he was taken to the Bastille. A few days later, Francis fled again, thanks to a rope thrown out of his sister's window.

The conflict was provoked by the misapplication of the last edict of pacification and by a conflict between Navarre and the lieutenant-general of the king in Guyenne, a province in which Henry was governor. During the conflict, Margaret rather took the side of her husband. It lasted briefly (1579-1580), thanks in part to the queen of Navarre who suggested calling her brother Alençon to lead the negotiations. They were rapid and culminated in the peace of Fleix.

Her work was dedicated to Brantôme, and it consisting of an autobiography from her infancy to 1582. The Memoirs were published posthumously in 1628. Queen Margaret was also visited by Writers, beginning with the faithful Brantôme, but also Honoré d'Urfé, who was no doubt inspired by Margaret to create the character of Galathee in L'Astrée, and Joseph Scaliger, who visited Usson in 1599.

When in June 1583 she fell sick, rumors claimed she had been pregnant with Champvallon. Henri III was soon scandalized by her reputation and behavior, and expelled her from the court, an unprecedented measure that made scandal in Europe, because Margaret's departure was accompanied by humiliations. The Queen's court was stopped by the Henry III's guards and some of her servants was arrested and interrogated by the King himself, especially about a possible birth of a bastard child by Jacques de Harlay.

On 13 April 1584, after long negotiations, Margaret was allowed to return to her husband's court in Navarre, but she received an icy reception. The situation got worse. In June 1584 her brother Francis died and she missed her most valuable ally. With Alençon's death Henry of Navarre became heir presumptive to the French throne and he was under increased pressure to produce an heir. In 1585, his new lover Diane d'Andouins, nicknamed La Belle Corisande, pressed the King of Navarre to repudiate Margaret, hoping to be married to him.

In 1585, with an unprecedented gesture for a Queen of the sixteenth century, Margaret abandoned her husband. She rallied the Catholic League, which united as well the intransigent Catholics with the people hostile to the policy of her family and her husband. Determined to overcome her difficulties, Margaret masterminded a coup d'état and seized power over Agen, one of her appanages. The Queen of Navarre spent several months fortifying the city. Recruiting troops, she sent them to the assault of the cities around Agen.

On 13 October 1586, Margaret was imprisoned by her brother Henry III in the castle of Usson, in Auvergne. D'Aubiac was executed, despite Catherine de' Medici's wish, in front of Margaret. Margaret assumed she was going to die and in a "farewell" letter to the Queen-Mother, she asked that after her execution a post-mortem be held to prove that she was not, despite gossip, pregnant with d'Aubiac's child.

But suddenly, her gaoler, the Marquis de Canillac, switched from the royal side in the civil war to that of the Catholic League and released her in early 1587. Rumors at the court of France reported that she seduced him, but most probably he was bought by her. Her freedom suited the League perfectly: her continued existence guaranteed that Henry of Navarre would remain without an heir.

Despite the acquisition of freedom, Margaret decided to stay in the castle of Usson, where she spent eighteen years. Of her life in Usson there was very few reliable information, so a lot of legends gathered around it. Here she learned of her mother's death and of her brother Henry III's assassination in 1589. Her husband, Henry of Navarre, became King of France under the name of Henri IV. He was, however, not accepted by most of the Catholic population until he converted four years later.

By 1593, Henry IV first proposed to Margaret an annulment of their marriage. Margaret resumed contact with him to try to correct her financial situation. Her sterility was proven but she knew that the new King needed a legitimate son to consolidate his power. For this, he needed the support of his wife because he wished to marry again.

The main action of william Shakespeare's early comedy Love's Labour's Lost (1594–1595) is based on an attempt at reconciliation, made in 1578, between Margaret and Henry.

The negotiations began after the return of peace and Henry IV's return to Catholicism. To support the invalidity of the marriage with the pope, the King and Margaret put forward the sterility of their couple, their consanguinity, and the formal defects of the marriage. During the talks, the financial situation of the queen improved, but Henry thought of marrying his mistress, Gabrielle d'Estrees, mother of his son, César, who was legitimized in 1595. Margaret refused to endorse a dishonorable remarriage: "It is repugnant to me to put in my place a woman of such low extraction and of so impure a life as the one about whom rumor speaks."

So she stopped the negotiations, but after the providential death of Gabrielle from eclampsia, Margaret returned to her demand for reasons of conscience, in exchange for strong financial compensation and the right to retain the use of her royal title. Clement VIII pronounced the cancellation bull on 24 October 1599. Later, on 17 December 1599, the Archbishop of Arles pronounced the annulment of Henry's marriage to Margaret of Valois. A year later Henry IV married Marie de' Medici, who nine months later gave him a son.

In 1605, after nineteen years in Usson, Margaret made her return to the capital. She has changed little - at least as far as her tastes are concerned; as for the physical, when she became "horribly stout", according to Tallemant des Réaux.

In 1606 she managed to win the lawsuit against her nephew and gained the entire maternal inheritance. After this, Margaret named her universal heir the dauphin Louis. This was an extremely important political move for the Bourbon family, as it made official the dynastic transition between the Valois family, of which Queen Margaret was the last legitimate descendant and that of Bourbon dynasty, just settled on the throne of France.

It only strengthened the friendship that had been created with Queen Marie de' Medici, to delegitimize the claims of Henriette d'Entragues, sister of Charles of Valois and lover of Henry IV, who claimed that her son was the legitimate heir for a King's promise of marriage. She often helped plan events at court and nurtured the children of Henry IV and Marie. In 1608, at the birth of Prince Gaston of France, Future Duke of Orleans, she was chosen by the King himself to be the godmother of new born.

On 13 May 1610, Queen Margaret also attended Marie's coronation to Saint Denis. The following day, Henri IV was assassinated by the hand of the fanatic monk François Ravaillac and Marie de' Medici obtained the regency for the minor child.

The regent entrusted various diplomatic roles, including the reception of foreign ambassadors at court and in the Estates General in 1614, in which Margaret was charged with negotiating with clergy representatives. This was her last public assignment.

Early in March 1615, Margaret was dangerously ill. She died in her Hostel de la Reyne Marguerite, on 27 March 1615. "On March 27 – wrote Paul Phélypeaux de Pontchartrain – there died in Paris, Queen Margaret, the sole survivor of the race of Valois; a Princess full of kindness and good intentions for the welfare and repose of the State".

By 1630, after Day of the Dupes, Cardinal Richelieu and his historians initiated a campaign against Marie de' Medici, a systematic discrediting of all women and their political role revived Margaret's black legend.

The 1845 novel of Alex Andre Dumas, père, La Reine Margot, is a fictionalised account of the events surrounding Margaret's marriage to Henry of Navarre.

Margaret is portrayed by Constance Talmadge in D.W. Griffith's 1916 film Intolerance.

Margaret of Valois also has a major role in the Meyerbeer opera Les Huguenots. This was one of Joan Sutherland's signature roles and she performed it for her farewell performance for the Australian Opera in 1990.

The novel was adapted into a 1994 French film, La Reine Margot in which the role of Margaret was played by the popular French Actress Isabelle Adjani.

On the other hand, well-established in the Auvergne and well-informed, she did not fail to spot the schemes of the Count of Auvergne, bastard son of King Charles IX of France and uterine brother of Henriette d'Entragues – a mistress evicted by King Henry IV. Duly informed, the King ordered in 1604 the capture of the conspirator and the confiscation of all his property. Queen Margaret ought in her time to have inherited from Auvergne a property belonging to her mother, Catherine de' Medici, who had disinherited her from her brother Henry III's schemes for the benefit of this ally. Margaret initiated a long trial and the King allowed her to return to Paris to manage her legal case.

The book Médicis Daughter by Novelist Sophie Perinot (Thomas Dunne, 2015) offered a coming of age story of this youngest Valois Princess.

François Eudes de Mézeray, a 17th century Historian, invented the legend that Margaret was forced to marry the King of Navarre with a little push at the back of her head by her brother Charles IX. This is one of the anecdotes that created the myth of the "Reine Margot."

Between the 19th and 20th centuries some historians such as Count Léo de Saint-Poincy sought to rehabilitate the figure of the queen, trying to discern the scandals from reality, depicting it as a woman who challenged the turmoil of the civil war, and that she had never felt less than her brothers, even wanting to participate in the affairs of the kingdom, thus also addressing the political behavior of Margaret in addition to private life. However, these studies remained marginal and did not affect official texts.