The village of Zavarzino was founded in 1626. It had a church dedicated to John the Baptist, but after the 1917 revolution, the building was closed and repurposed as a club. In the 1980s, it became dilapidated and was demolished.

In 2004, an Orthodox parish reemerged in the settlement. A group of citizens long sought to build a prayer house. In 2011, a site was chosen on an elevation in the center of the settlement, where the church was laid.

On July 7, 2014, on the feast of the Nativity of the Prophet, Forerunner, and Baptist of the Lord John, Metropolitan Rostislav of Tomsk and Asinov conducted the Divine Liturgy at the John the Baptist Church in the village of Zavarzino, on the day of the church's patronal feast.