In the interwar period, it was quite common to build new and modernist prayer homes in Kaunas for all ethnic groups that had historically existed in the city until then.

Although in 1860 a wooden prayer house was built on this site, in 1930, on the occasion of the 500th anniversary of the death of Vytautas the Great, a new brick mosque project was established. A modernized mosque that has preserved the oriental style is the work of architects Vaclovas Michneviciaus and Adolfas Netyksas. It was the only religious building built in Kaunas during the jubilee year.

During the Soviet era, the building was turned into a circus, a library, and later - a warehouse. Over the course of history, the facade of the building hardly changed. After regaining independence, the mosque was returned to continue its original functions. Interestingly enough, during the reconstruction of the prayer hall, decorated walls with Arabic-style paintings were discovered and are now being preserved.