The first mention of Krakės is from the 14th century. The Krakės Manor was a property of Samogitian bishops between 1421 and 1842. The first church of Krakės was built at 15th century. Krakės is mentioned as a town in 1579. A women monastery of St. Catherine Order was established in Krakės in 1615 and run till 1945 (the wooden monastery burnt at that time), then reestablished in 1997. A market privilege was granted to Krakės in 1790. During 1863, Krakės was important center of the January uprising, on 28 April there was a battle against Russian imperial army. In 1863 and 1914 Krakės was devastated by fires.