In 1988, with national revival in Lithuania on the rise, the desire to learn and tell about the cruelties and crimes of the Soviet occupying regime and armed and unarmed anti-Soviet resistance in Lithuania was accentuated. Various non-governmental and state entities were established for this purpose, and they undertook studies of Stalinist crimes and collected information about victims of the regime. After the termination of the activities of the Lithuanian unit of the KGB in 1991 and with a view to preserving the archives of all special services, repressive organisations, and the Lithuanian Communist Party, the State Residents Genocide Centre of Lithuania (VLGGTC) was established by a 29 October 1992 resolution of the Lithuanian parliament. The centre was assigned the task of preserving, handling and studying the archives of special significance. On 26 November 1996, the Lithuanian government approved the provisional regulations of the centre and appointed historian and former anti-Soviet resistance activist Juozas Arvydas Starkauskas as the interim head of the centre.
On 1 June 1993, the Lithuanian parliament resolved that archive documents of special significance should be entrusted to the Lithuanian Archives Directorate-General. On 16 July 1993, the VLGGTC underwent reorganisation to become the Genocide and Resistance Research Centre of Lithuania (LGGRTC) comprising two institutes: the Lithuanian Genocide and Resistance Research Institute and the Lithuanian Genocide Victims Remembrance Institute. Vytautas Skuodis, an anti-Soviet resistance activist and underground publisher, was appointed director general of the centre. On 17 November 1994, the Commission for the Rights of Participants in the Resistance Movement was merged with the LGGRTC and the centre was assigned the task of issuing IDs to those who had participated in the resistance.
To ensure that there was a single entity forming research policies and coordinating the research in this field conducted by all parties involved and that funds from the national budget fund were used more efficiently, the LGGRTC was reorganised once again on 13 February 1997 and the Centre for the Research of Repression in Lithuania (which began operating in the Lithuanian Philosophy, Sociology and Law Institute in 1992) and the Lithuanian Museum of Genocide Victims (which began operating in the former KGB building in October 1992) were merged with the centre. In 1998 the Foundation for Lithuanian Genocide and Resistance Research and for Victims Support and Remembrance was established within the framework of the LGGRTC. The foundation provides financial assistance to victims of repression and participants in the resistance movement and finances key remembrance programmes.
The currently enforced Law on the Genocide and Resistance Research Centre of Lithuania was passed on 5 June 1997, and the regulations of the Centre were approved on 11 November 1997.
Dalia Kuodytė, historian, head of the Museum of Exile and Resistance in Kaunas and editor-in-chief of the magazine Laisvės kovų archyvas (An Archive of the Struggle for Freedom), became director general of the reorganised LGGRTC in 1997. After Ms Kuodytė was elected an MP in 2008, Teresė Birutė Burauskaitė, an anti-Soviet resistance activist, former head of the Centre for Research of Repression in Lithuania, and head of the Archive Index Unit (after the Centre for Research of Repression in Lithuania was merged with the LGGRTC), became the new director general of the LGGRTC by decision of the Lithuanian parliament dated 20 January 2009.