The church was built between 1841 and 1844 according to the design of provincial architect Karl Tursky and was consecrated by Bishop Athanasius of Tomsk and Yenisei. The funds for construction were provided by the Old Believer community of Tomsk, with the main donor and patron being the Old Believer P. I. Pozdeev.

Later, two chapels were added to the church: the northern in honor of St. Charalambos the Martyr and the southern in honor of St. Demetrius of Thessalonica. Two single-class schools operated at the church: the Resurrection Men's and Women's Schools. In the early 20th century, merchant N. Tikhonov planted a garden around the church.

In August 1937, Bishop Seraphim (Shamshin) was arrested and shot on September 17. The Bolsheviks vandalized the church, destroying icons, books, and archives. The church effectively ceased operations on September 27, 1937, by the decision of the Tomsk City Council, and the official order for closure was issued on February 8, 1940. By this time, all churches in the Tomsk diocese had been closed, and it ceased to exist. By 1938, not a single one of the 41 prayer buildings in the city was functioning.

The Holy Trinity Church was turned into a storage facility for Zagotzerno, and later into the office of the automobile column 'Sibkhoztrasa'. Church utensils were handed over to the state fund or thrown away, and books and icons were burned. The building suffered damage: crosses were removed, the walls of the southern chapel were partially destroyed, and doors, floors, and window frames were torn off.

After the war, in 1945, the Trinity Church was allowed to reopen. It was restored with public funds. An 18th-century iconostasis was brought from the church in the village of Zorkaltsevo. The restored cross on the bell tower was decorated with mirrors instead of gold, which have survived to this day. On February 15, 1946, the church was consecrated again according to Orthodox rites and ceased to be Old Believer.

Until the early 1990s, the Peter and Paul Cathedral and the Holy Trinity Church remained the only functioning Orthodox churches in Tomsk.

Today, a Sunday school and library operate at the church. On its territory, there is a tombstone monument to the famous Tomsk entrepreneur and philanthropist E. I. Korolev.