Fan Noli was born in 1882 in the Albanian village of Ibrik Tepe (Albanian: Qytezë), Eastern Thrace (then part of the Ottoman Empire) as Theofanes Stylianos Mavromatis. He was an Albanian of the Eastern Orthodox faith. He came from an Orthodox Albanian community who had fled socio-political turbulence (18th century) from what is today southern Albania and resettled in Thrace in areas that had been depopulated due to previous conflicts. During his youth, Noli received his education from Greek elementary and secondary schools. As a young man, Noli wandered throughout the Mediterranean Basin, living in Athens, Greece, Alexandria, Egypt and Odessa, Russia, and supported himself as an actor and translator. As well as his native Albanian, he spoke many languages such as Greek, English, French, Turkish, and Arabic. Having been a Teacher in Athens, Noli went abroad to Egypt in 1903 and worked as a Teacher in Greek schools of Alexandria using the name Theophanis Mavromatis and did not espouse Albanian national sentiments. Later in his work as a Teacher and in Egyptian theater Noli embraced Albanian national sentiments. Through his contacts with the Albanian expatriate movement, he became an ardent supporter of his country's nationalist movement and moved to the United States in 1906. He first worked in Buffalo, New York, in a lumber mill and then moved to Boston, Massachusetts and worked as an operator on a machine which stamped labels on cans.

In 1908, Noli began studying at Harvard, completing his Bachelor of Arts degree in 1912. During April 1912 Vatra (Hearth) an Albanian American diaspora organisation was founded with Noli and Faik Konica serving as its Leaders and advocating for Albanian sociopolitical self determination with the Ottoman Empire. He returned to Europe to promote Albanian independence, setting foot in Albania for the first time in 1913. Noli returned to the United States during World War I, serving as head of the Vatra organization, which effectively made him leader of the Albanian diaspora. His diplomatic efforts in the United States and Geneva won the support of President Woodrow Wilson for an independent Albania and, in 1920, earned the new nation membership in the fledgling League of Nations. Though Albania had already declared its independence in 1912, membership in the League of Nations provided the country with the international recognition it had failed to obtain until then.

He earned degrees at Harvard (1912), the New England Conservatory of Music (1938), and finally his Ph.D. from Boston University (1945). He was ordained a priest in 1908, establishing thereby the Albanian Church and elevating the Albanian language to ecclesiastic use. He briefly resided in Albania after the 1912 declaration of independence. After World War I, Noli led the diplomatic efforts for the reunification of Albania and received the support of US President Woodrow Wilson. Later he pursued a diplomatic-political career in Albania, successfully leading the Albanian bid for membership in the League of Nations.

In 1921, Noli entered the Albanian parliament as a representative of the liberal pro-British "People's Party" (Albanian: Partia e Popullit), the chief liberal movement in the country. The other parties were the conservative pro-Italian "Progressive Party" (Albanian: Partia Përparimtare) founded by Mehdi Frashëri and led by Ahmet Zogu, and "Popular Party" (Albanian: Partia Popullore) of Xhafer Ypi. The conservatives of Zogu would dominate the political scene. A Congress of Berat in 1922 was convened to formally lay the foundations of an Albanian Orthodox Church which consecrated Fan Noli as Bishop of Korçë and primate of all Albania while the establishment of the church was seen as important for maintaining Albanian national unity.

Noli served briefly as foreign minister in the government of Xhafer Ypi. This was a period of intense turmoil in the country between the liberals and the conservatives. After a botched assassination attempt against Zogu, the conservatives revenged themselves by assassinating another popular liberal Politician, Avni Rustemi. Noli's speech at Rustemi's funeral was so powerful that liberal supporters rose up against Zogu and forced him to flee to Yugoslavia (March 1924). Zogu was succeeded briefly by his father-in-law, Shefqet Vërlaci, and by the liberal Politician Iliaz Vrioni; Noli was named prime minister and regent on July 17, 1924.

In 1928, KONARE changed its name to "Committee of National Liberation" (Albanian: Komiteti i Çlirimit Kombëtar). Meanwhile, in Albania, after three years of republican regime, the "National Council" declared Albania a Constitutional Monarchy, and Ahmet Zogu became king. Noli moved back to the United States in 1932 and formed a republican opposition to Zogu, who had since proclaimed himself "King Zog I". Over the next years, he continued his education, studying and later teaching Byzantine music, and continued developing and promoting the autocephalous Albanian Orthodox Church he had helped to found. While in exile, he briefly allied with King Zog, who fled Albania before the invading Italians in 1939, but was unable to set a firm anti-Axis, anti-Communist front.

After the war, Noli established some ties with the communist government of Enver Hoxha, which seized power in 1944. He unsuccessfully urged the U.S. government to recognize the regime, but Hoxha's increasing persecution of all religions prevented Noli's church from maintaining ties with the Orthodox hierarchy in Albania. Despite the Hoxha regime's anticlerical bent, Noli's ardent Albanian nationalism brought the bishop to the attention of the U.S. Federal Bureau of Investigation. The FBI's Boston office kept the bishop under investigation for more than a decade with no final outcome to the probe.

In 1945, Fan S. Noli received a doctor's degree (Ph. D) in history from Boston University, writing a dissertation on Skanderbeg. In the meantime, he also conducted research at Boston University Music Department, publishing a biography on Ludwig van Beethoven. He also composed a one-movement symphony called Scanderbeg in 1947. Toward the end of his life, Noli retired to Fort Lauderdale, Florida, where he died in 1965. The branch of the Albanian Orthodox Church that he had governed eventually became the Albanian Archdiocese of the Orthodox Church in America.

Fan Noli is venerated in Albania as a champion of literature, history, theology, diplomacy, journalism, music and national unity. He played an important role in the consolidation of Albanian as the national language of Albania with numerous translations of world literature masterpieces. He also wrote extensively in English: as a scholar and author of a series of publications on Skanderbeg, Shakespeare, Beethoven, religious texts and translations. He produced a translation of the New Testament in English, The New Testament of our Lord and Savior Jesus Christ from the approved Greek text of the Church of Constantinople and the Church of Greece, published in 1961.

Fan S. Noli is depicted on the obverse of the Albanian 100 lekë banknote issued in 1996 though the banknote itself has ceased being legal tender since December 31, 2008.