The II Vatican Council charged "competent territorial Church authorities" to make decisions on many local Church issues. The territorial Lithuanian Church authorities were registered by a judicial act of Bishop Petras Maželis on February 10, 1965. While the majority of the members were still the diocesan heads without episcopal ordination they carried the name of the Board of Lithuanian Diocesan Ordinars. With the increase of the number of bishops the Board was reorganized into the Lithuanian Bishops' Conference and is so called in the documents of the Holy See. The Lithuanian Bishops' Conference was mentioned for the first time in the year-book Annuario Pontificio in 1971.
In 1966 after the death of the president of the Board of Lithuanian Diocesan Ordinars Bishop of Telšiai Petras Maželis, Bishop Juozas Matulaitis Labukas (19 10 1894 – 28 05 1979) was elected for the post of a new president. Bishop Juozas Matulaitis Labukas signed the aprobate (imprimatur) of the Lithuanian edition of the New Testament as a President of the Board of Lithuanian Diocesan Ordinars. After his death the post was passed to Bishop Liudvikas Povilionis (Archbishop since 1984) (08 09 1910 – 09 08 1990). On May 20, 1982 he signed the aprobate (imprimatur) of the Lithuanian translation of Roman Missal as the President of the Lithuanian Bishops' Conference. In 1988 Vatican granted Archbishop Povilionis’ request to be dismissed from his post.
During the process of change in the Soviet Union, the beginning of free and unrestrained activities of the Lithuanian Church was marked by the declaration of the documents of Lithuanian hierarchy in August-September 1988. These were: the public announcement of the Cardinal Vincentas Sladkevičius, the announcement of the Episcopate of Lithuanian Catholics – a motion and the declaration of the Hierarchy of the Lithuanian Catholic Church (published in the Catholic year-book in 1989). The return of the freedom of the Church stipulated a new stage of the development of the Lithuanian Bishops' Conference.
One of the subdivisions of the Conference was rather active even during Soviet times, considering, of course, the restrains of the Church at that time. The Liturgical Commission of Lithuanian Dioceses was instituted on February 10, 1965. Since the very beginning it was subordinate to the Lithuanian Bishops' Conference (the Board of Lithuanian Diocesan Ordinars) and the Vatican Congregation of Sacraments and Divine Worship. The Liturgical Commission of Lithuanian Dioceses prepared translations of liturgical books into Lithuanian and also contributed to the preparation and publishing of the Church publications. Msgr. Česlovas Krivaitis served as president of the Commission during 1965 – 1979. Fr. Vaclovas Aliulis MIC was the president during 1980 – 1990. Beside the Liturgical Commission of Lithuanian Dioceses there were also commissions instituted for special jubilees and celebrations. Those commissions, opposite to the Liturgical Commission were temporary and not always active during Soviet times. On January 3, 1991 Bishop Juozas Preikšas became president of the reorganized Commission.
Cardinal Vincentas Sladkevičius (20 08 1920 – 28 05 2000), still Archbishop of Kaunas, was president of the Lithuanian Bishops' Conference during 1988 – 1993.
On October 15, 1993 the president of the Conference became Archbishop of Vilnius Audrys Juozas Bačkis. According to the statutes of the Lithuanian Bishops' Conference a president is elected for a three year period and for not more than two terms of office. Archbishop of Kaunas Sigitas Tamkevičius was elected for the post of the president of the Conference on November 3, 1999. On September 20, 2002 Archbishop of Vilnius, Cardinal Audrys Juozas Bačkis was elected for the post of the president of the Conference. Archbishop of Kaunas Sigitas Tamkevičius became the vice-president of the Conference.
The last election has been held on September 20, 2005 and Archbishop of Kaunas Sigitas Tamkevičius was elected for the post of the president of the Conference. Archbishop of Vilnius, Cardinal Audrys Juozas Bačkis became the vice-president of the Conference.
The regaining of the freedom of the Church and the reestablishment of Church institutions brought about the institution of new commissions, councils and other subdivisions in the structure of the Conference. The Permanent Council of Bishops was instituted on October 3, 1993. The Secretariat started its work in Vilnius in 1994. Due to the move of the Secretariat to Vilnius, Msgr. Vytautas Kazlauskas resigned from the post of general secretary. The post was given to Rev. Gintaras Grušas on June 30, 1994. Bishop Jonas Boruta SJ was elected for the post of secretary general on August 12, 1997 for a three year term of office.
On September 20, 2002 and 2005 Msgr. Gintaras Grušas was re-elected for the post of secretary general.