In 1626, a brick church was built and 20 tithes of land were donated by the Čekiškės landowner Jurgis Gedgaudas Mackevičius. On August 13, 1799, the church burned down, leaving only the brick walls.
In its place, on the initiative of the pastor, Father Bonaventuras Miknevičius (he wrote a hymn about the Čekiškė church), in 1821 the current church was built and extended, and a tower was added. In 1805 there was a shelter near the church. In the 19th century (until 1863), a parish school operated. Aleksandras Vytartas, the vicar of Čekiškė, was shot for reading the 1863 insurgents' appeal in the church.
The church was rebuilt in 1935. It has classicist features, a basilica, with side extensions and a tower. The interior has 3 naves. The high altar was made in Grodno and brought by ship to Vilkija (built in 1806). The high altar features a group of sculptures carved from oak, depicting the taking down of Christ from the cross. This is a work of an unknown German master from the 16th century, which has no analogues in Lithuania. In 1806, a pulpit was installed, and in 1819 a new sacristy was built. The churchyard fence is made of stone masonry, with a metal lattice gate. In its corner stands a brick bell tower.
In 1996, a chapel pillar was erected in the churchyard to commemorate the signatory of the February 16 Act, Prof. Pranas Dovydaitis (1886–1942), on the occasion of the centenary of his birth.
On July 16, 2017, the parish celebrated the 400th anniversary of its establishment.