The independence of Lithuania regained in 1990 opened possibilities to carry out research on religion unrestricted by antireligious policy of the Soviet Union. Soon the country saw a gradual development of confessional and non-confessional research on religion and the growth of a community of researchers of religion. In a meeting held on October 1, 2001 researchers of religion decided to establish the Lithuanian Society for the Study of Religions (LSSR) – a non-governmental organization aiming to unite researchers engaging in non-confessional research of religion and religion-related phenomena. Gintaras Beresnevičius, Pranas Vildžiūnas, Miglė Krūminaitė, Andrius Navickas, Juozas Šorys, Audrius Beinorius, Jakaterina Lavrinec, Loreta Poškaitė, Vladimir Korobov and Dainius Razauskas took part in the founding meeting of the LSSR. Historian of religion, researcher of the Baltic pre-Christian religion Gintaras Beresnevičius was elected as a chairperson of the Society. The planned activities included the development of religious studies based on scientific approaches as opposed to confessional or atheistic perspectives. Another aim was to introduce the Lithuanian society to works of Western researchers of religion and methods they apply, in this way filling the gap in the Lithuanian academic discourse of this area and contributing to the development of open society in Lithuania. Shortly after the Society was founded, its first conference “Erosion of Idols” took place on December 7, 2001. Unfortunately, the Society did not develop its activities actively and they halted completely when its chairperson Gintaras Beresnevičius passed away in 2006.

In a meeting held on June 6, 2011, members of the Society decided to renew its activities. Under the leadership of sociologist of religion Milda Ališauskienė, the renewed Society attracted new members who represented a wider range of disciplines dealing with religion, and significantly broadened areas and scale of its activities. 

The Society focused on strengthening its international connections and an international dimension of its activities. In 2012 the LSSR became a member of the International Association for The History of Religions (IAHR) and the European Association for the Study of Religions (EASR). The second national academic conference of the LSSR “Interdisciplinary Studies of Religion in Lithuania: Problems and Tendencies” took place in 2012. It was followed by the international academic conference “Religious Diversification Worldwide and in Central and Eastern Europe” organized in collaboration with the International Study of Religion in Eastern and Central Europe Association (ISORECEA), and other national and international academic conferences. 

Since 2015 the LSSR has paid much attention to the dissemination of research results of the Lithuanian community researchers of religion and popularization of non-confessional research on religion in the Lithuanian society. In collaboration with various culture institutions, the LSSR organizes public lectures that aim to raise awareness of the public of relevant research of members of the Society and other scholars and to provide public commentaries on religion-related issues of the day. 

Since 2018, under the leadership of anthropologist of religion Rasa Pranskevičiūtė-Amoson, the LSSR has been searching for new areas of activities and ways of action. Representing researchers of religion from various Lithuanian high education and research institutions, in 2019 the LSSR started issuing proposals to bodies of science administration, providing expert opinions to the highest state institutions, and making comments on societal processes related to religion.  The LSSR is pleased with the growing community of Lithuanian researchers of religion and joining young researchers who will enrich Lithuanian religious studies with new perspectives and fields of research.