The name FALINTIL is an acronym of its full name in Portuguese, Forças Armadas da Libertação Nacional de Timor-Leste. In English this translates as 'The Armed Forces for the National Liberation of Timor Leste'.
At the time of the Indonesian invasion of East Timor in 1975 FALINTIL consisted of 2,500 regular troops, 7,000 who had some Portuguese military training, and 10,000 who had attended short military instruction courses, a total of 20,000.
The first Commander of FALINTIL was Nicolau Lobato. Lobato was killed during a battle with the Indonesian armed forces in 1978 and Xanana Gusmão was elected as his replacement during a Secret National Conference in Lacluta, Viqueque in 1981. This meeting in 1981 also saw the formation of the Revolutionary Council of National Resistance (in Portuguese Conselho Revolucinario de Resistencia Nacional or CNNR) which was the first step in uniting the different resistance movement factions under one umbrella organisation.
On the 20th of June 1988 the National Resistance of East Timorese Students or RENETIL (Resistencia Nacional dos Estudantes de Timor-Leste) was created in Indonesia, reporting directly to FALINTIL and its Commander in Chief Xanana Gusmão. On the 31st of December 1988 Gusmão officially announced that FALINTIL was now the non-partisan armed resistance wing of the unified resistance movement, which was now to be known as the National Council of Maubere Resistance or CNRM (Conselho Nacional da Resistencia Maubere).
The month of May in 1990 was significant in the history of FALINTIL and the overall resistance movement. Between the 23rd and the 28th of May 1990, CNRM held an extraordinary meeting for the purposes of restructuring the entire resistance movement. It was during this conference that Gusmão officially resigned from the FRETILIN party, whilst remaining Commander-in-Chief of FALINTIL and the president of CNRM. This meeting also saw the formation of the Clandestine Front, which came about from the recognition that FALINTIL, the armed resistance, had been significantly weakened by years and years of guerilla activity against the Indonesian military and the formation of the Clandestine Front was a strategy aimed at the organisation of the population against the occupying Indonesian forces. These events saw an upsurge in activity against the unified resistance movement by the occupying forces, which saw many of the leaders flee to the mountains or overseas, and led ultimately to the arrest of Gusmão on the 20th of November 1992. Ma'Huno, who had been on FRETILIN's steering committee in the restructure of the resistance movement became the leader of the resistance only to be arrested himself a short time later on the 5th of April 1993. Nino Konis Santana replaced the arrested Ma'Huno as leader on the 25th of April 1993 and by September of that year all factions of the resistance accepted Santana as leader of the overall movement and appointed Taur Matan Ruak as commander of FALINTIL. Under Santana's leadership the restructuring started by Gusmão was further reinforced under the CNRM umbrella with Santana as leader of the Executive Council of "the Struggle", Ruak in charge of FALINTIL, and a man called Sabalae taking charge of the Clandestine Front.
Throughout the 1990s the occupying Indonesian forces stepped up their actions against the resistance and factional troubles between FRETILIN and other resistance organisations plagued the CNRM, with FRETILIN members signing a document against the leadership of Santana. Sabalae, the leader of the Clandestine Front, disappeared in June 1995. Gusmão remained supreme leader of CNRM and Commander in Chief of FALINTIL despite being incarcerated in an Indonesian prison. In 1998 Santana died in an accident and the FALINTIL commander, Ruak, was elected as leader of "the Struggle", whilst also remaining operational commander of FALINTIL. In April of 1998 during the National Convention of East Timorese Living Abroad, held in Portugal, the National Council of Timorese Resistance (Conselho Nacional Resitencia Timorense - CNRT) was formed, replacing CNRM and reinforcing the previous attempts to unify all the factions of the resistance struggle against Indonesia.
The last Commander in Chief of FALINTIL was Commander Taur Matan Ruak.