Klepočiai was founded during the Valakia Reform as a settlement of foresters and scullery manufacturers by the Geluža stream. Klepočiai is mentioned in historical sources in 1641. It belonged to the Lieponiai Manor.
The Klepočiai section of the Lieponiai-Valkininkai Forestry District was divided into 9 bars. The village was inhabited by a land surveyor and 21 followers, whose duty was to protect beavers in the Valkininkai territory, which extended two miles from Varėna. During the 1654–1667 war between the Republic of Lithuania and Moscow, the village fell into decline. It was restored in the 18th century. In 1862, the Vilnius–Grodno railway was built through the village. At the end of the 19th century, the village belonged to the Valkininkai rural municipality of Trakai County. In 1920 and 1923, In 1943-1944, battles took place near Klepočiai over the Valkininkai-Rūdiškės railway section. After the region was occupied by the Poles, in 1924 a Lithuanian school of the "Rytas" society was opened in the village.
In 1943-1944, a German military garrison settled in Klepočiai, and Soviet partisans carried out bombings on the Rūdiškės-Klepočiai railway section.