Established as the Diocese of Vilnius in the 14th century, it was elevated to the rank of a metropolitan archdiocese by Pope Pius XI on October 28, 1925.

The archdiocese's motherchurch and thus seat of its archbishop is Cathedral-Basilica of St. Stanislaus and St. Ladislaus in Vilnius; it also houses a minor basilica in Trakai.

The Archdiocese owes its foundation to Grand Duke Jogaila of Lithuania, who Christened Lithuania in 1387 and sent Dobrogost, Bishop of Poznań as ambassador to the Pope Urban VI with a petition for the erection of an episcopal see at Vilnius and the appointment of Andrzej Wasilko (former bishop of Siret and confessor of Elisabeth of Hungary) to fill it.

Among his successors were: Piotr Krakowczyk of Kustynia (1414–1421), whom Pope Martin V invested with full powers to bring back the Orthodox of Lithuania to the Catholic Church; Matthias of Trakai (1421–1453), a Lithuanian, who sent representatives to the Council of Basel and set up the Inquisition to combat the Hussites, founded many churches and strenuously defended the rights and privileges of the Lithuanians.

Prince Jerzy Radziwiłł (1581–1591) fostered the Alma Academia et Universitas Vilnensis Societatis Iesu, founded a seminary, under the direction of the Jesuits, introduced the regulations of the Council of Trent, and having been made a cardinal, was transferred to the Diocese of Kraków in 1591.

At his death in 1594, the clergy were divided into factions on the choice of a successor, until Sigismund III nominated Benedict Wolna (1600–1615), who exerted himself efficaciously for the canonization of Saint Casimir Jagiellon, in whose honour the first stone of a church was laid it Vilnius in 1604.

His successor, Eustachius Wollowicz (1616–1630), founded hospitals, invited the Canons Regular of the Lateran to Vilnius, and energetically combated the Protestants and the Orthodox.

Prince Ignacy Jakub Massalski (1762–1794) encouraged the reform of the clergy and devoted his immense fortune to the churches of his diocese.

After his death the chapter became involved in a conflict with Stanisław Bohusz Siestrzeńcewicz, the Catholic Metropolitan Archbishop of Mohilev (from 1798 to 1925 Vilnius was a suffragan see of the Archdiocese of Mohilev, the effective see was in Saint Petersburg), who used his metropolitan rights and forced, upon the chapter, the nominee of Hieronim Stroynowski as administrator and later Bishop (1808–1815), upon whose death he arrogated to himself the government of the diocese with the title of primate of Lithuania.

In 1828 Andreas Klagiewicz was appointed administrator; he was sent to the interior of Russia during the Insurrection of 1831, returned in 1832, was preconized Bishop of Vilnius in 1839 and took possession of the see on June 28, 1841.

The chapter elected John Cywinski as vicar suffragan; he saw the University of Vilnius closed, the clergy and churches of his diocese despoiled of their property.

His place was taken by Baron Edward Ropp, who set about organizing the Catholic movement in the diocese, thereby incurring the hostility of the Russian Government.

Among the most famous may be mentioned George Casimir Ancuta (d. 1737), author of "Jus plenum religionis catholicae in regno Poloniaw", showing that the Protestants and Orthodox had not the same rights as the Catholics.

The cathedral, dedicated to the Blessed Trinity, St. Stanislaus and St. Ladislaus, was erected in the place of a demolished pagan sanctuary in virtue of a Papal Bull of 12 March 1387.

The Bernardines undertook at Vilnius, in 1469, the construction of a wooden church, rebuilt in stone in 1500; it was burnt down in 1794 and restored in 1900; this order was forced to leave the diocese in 1864.

In the early 20th century the Roman Catholic diocese of Vilnius had 1,420,000 faithful distributed among 23 rural deaneries as follows: Besides the cathedral parish the city of Vilnius contains those of St. John Baptist, the Holy Spirit, St Teresa, Saints Philip and James, St. Raphael the Archangel, St. Francis of Assisi, All Saints, the Holy Apostles Peter and Paul.