The village of Sannikovo is first mentioned in the land books of the 16th century as the estate of the Borisov family. At that time, there was a church dedicated to Saint Nicholas the Wonderworker.

In 1864, a stone church was built in the name of the Transfiguration of the Lord with an altar dedicated to Saint Nicholas the Wonderworker in the warm church. The village belonged to the noblewoman Maria Rostova. By the end of the 18th century, Sannikovo had about 60 households, and both a church and a parish school were functioning.

The church was fully completed in 1897 and had two altars: the main one in the cold church in honor of the Transfiguration of the Lord and the altar of Saint Nicholas the Wonderworker in the warm church. The bell tower reached a height of 35 meters and had five bells, the largest of which weighed 4 tons.

The parish of the Sannikovo church included four more villages: Stepan'kovo, Berezovka, Saksino, and Ivan'.

During the Soviet era, a collective farm called 'Organized Labor' was established here, and the church was destroyed in 1936. The school operated until 1969. In the 1930s, the local collective farm joined the 'Struggle' collective farm with its central estate in the village of Stepan'kovo, and the school became part of the Stepan'kovo eight-year school.

Today, the village of Sannikovo is part of the Borisoglebsk rural settlement. It has 80 houses, and according to the 2010 census, 58 people live here. In 2013, the restoration of the Spaso-Transfiguration Church began, which brought joy to the local residents.