The history of the Islamic community of Kaunas can be traced to the arrival of Muslim Lipka Tatars in the Grand Duchy of Lithuania in the 15th century.

The territory of the Muslim Cemetery was divided into two parts: Originally there was a wooden mosque on the banks of the Neman river.

However, during French invasion of Russia in the winter of 1812, Napoleonic troops crossed the city of Kaunas and set the wooden building afire.

It had no minaret, instead only a small tower adorned the roof peg with the symbol of the golden crescent with a star.

There was also no front court, instead a two-meter deep, fenced-off front yard set behind the double-door entrance which was decorated with a memorial plaque, with the Muslim testimony of faith Shahada written on it: lā ʾilāha ʾillā -llāhu muḥammadun rasūlu -llāhi (There is no deity but Allah, Muhammad is the messenger of Allah).

Nevertheless, the prayers well attended, because among the Russian garrison of the Kaunas Fortress were 2000 Muslim soldiers, who visited the mosques on Fridays.

[4][5] The mosque was designed by Vaclovas Michnevičius (1866-1947) and Adolfas Netyksas, who followed a modernist style with respect to the elements of Islamic architecture.

[8] Since the independence of Lithuania, the Kaunas City Muslim Religious Community (Lithuanian: Kauno Miesto Musulmonų Religinė Bendruomenė) owns the mosque.

Most believers who visit the mosque are foreign students from throughout the world who study in Kaunas' universities and businessmen from Central Asia.