It was the second Catholic diocese in ethnic Lithuanian parts of the Grand Duchy of Lithuania.

On July 3, 1848, it gained territory from the persisting then Diocese of Vilnius, now Lithuania's other Metropolitan see.

The Apostolic constitution, issued by Pius XI, intended to structure the diocesan territories in accordance with the actual boundaries of Lithuanian Republic after the Declaration of Independence in 1918.

Due to fact, that claimed Lithuanian capital city Vilnius and the eastern parts of the country were seized by Polish troops in 1920 and annexed by Poland in 1922, Kaunas became not only the Temporary capital of Lithuania but also was promoted by Pope Pius XI on April 4, 1926, into the Metropolitan Archdiocese of Kaunas, initially with as suffragan sees Vilkaviškis and Telšiai in the new Lithuanian ecclesiastical province.

The then diocese of Vilnius was also elevated into a Metropolitan Archbishopric with its ecclesiastical province in Polish territory.