Founded in 2000, as a result of the nation's independence, its history can be traced, through the Faculty of Education, to the Portuguese colonial period, when the first public higher schools prepared for teachers appeared.

Forming the country's intellectual elite, it is also a national reference in teaching, research and extension, the tripods of higher education.

[2] It is a multilingual university, being the largest research center in Tetum, one of the two official languages of East Timor, but its classes are taught primarily in Portuguese.

[7] With the extinction of the only higher school in Timor, the island was left without training of minimum teaching staff, including for teaching Indonesian (the only official language allowed after the occupation), a fact that led the Indonesian government to recreate, in 1979, the General Course in its old structure, under the name Educational Course for Teachers;[5] the institution was fully transferred to UnTim when it was created, constituting the Faculty of Education.

[5] On October 1, 1986, in the midst of Indonesian occupation, on the initiative of the then governor Mário Viegas Carrascalão and the Loro Sae Foundation, "Universitas Timor Timur" (UnTim) was founded.

The university existed largely to train middle-level administrators, agricultural extension workers and secondary school teachers.

By 1998/99 UNTIM had nearly 4,000 students, with 73 permanent teaching staff, in three main faculties — Agriculture, Social & Political Sciences and Education & Teacher Training.

[8] In 1995–98, at a time of escalating instability in East Timor and Indonesia, Georgetown University and USAID established the first international assistance project for UNTIM.

Technical courses were based in a building in Becora, next to the Senior High School of Economics, and a campus in Hera, close to the University's Agriculture College.

In September 1999 when the Indonesian military and militia rampaged through East Timor destroying vital infrastructure, the education system was a major target for destruction.

After the destruction students again went to regional areas to teach classes in burnt out buildings to keep the children learning and the schools open.

Tight planning and active lobbying of donors by Dr Armindo Maia (acting rector and now Minister for Education, Youth and Cultural Affairs) and the then Minister for Education, Father Filomeno Jacob meant that the new university, despite its serious lack of resources, was able to commence teaching classes for 5,000 students and 1,500 bridging course students in November 2000.

[10] In 2016, there were 37 higher education courses, organized in nine faculties:[11] In addition to the university structure, there are still four research centers:[11] The East Timorese student associations that had been formed on the UNTIM campus and within Indonesia (ETSSC, IMPETTU and RENETIL) became the mainstay of the pro-independence campaign for the ballot and continued to be active afterwards.

A clandestine student organisation was formed in 1997 (the East Timor Youth Solidarity Organization, OSK-TL) to encourage non-violent resistance against Indonesian occupation.

RENETIL (Resistência Nacional dos Estudantes de Timor Leste) began as an organization of East Timorese students attending universities in Indonesia in 1988.

[12] ETSSC, IMPETTU and RENETIL continue to work to secure a democratic future for East Timor through education and training, community development, participation in the election process and other nation building programs.