The wooden Church of the Exaltation of the Holy Cross was located here in the middle of the XVII century. Ninety years later, it burned down, but was restored almost immediately. To the south-west of the wooden church, with the money of parishioners, a stone church was built on the embankment of the merchants of the Medvedev brothers in 1771.
In 1784, in Tobolsk, the water rose 11 yards and 7 vershkov, and the church was heavily flooded, there is even an inscription on the wall of the Holy Cross (Intercession) Church.
In the flood of 1794, the water rose above this inscription by 2 vershka.
The bell tower of the temple remained wooden for another thirteen years. In 1790, the north aisle of Simeon Stylite and his mother Martha was laid. In 1798, the construction was completed completely.
Wealthy citizens spared no expense for the needs of the temple. In May 1821, the Tobolsk merchants of the 1st guild, Simeon and Nikolai Pilenkov, gilded the crosses and heads of the church at their own expense, and painted the roof and domes with green paint. The interior of the church was decorated with alabaster bas-reliefs made by a master from Tara Semyon Sidelnikov.
In 1854 there was a big flood. The interior of the temple was saved by sealing with rubble. In 1859, the flood was repeated, but the church survived, people went to the service on wooden scaffolds.
Priests Konstantin Nedosekov, Alexander Grammatin, Vasily Serebrennikov, Peter Ponikarovsky served in the church in different years.
The parish of the church included the Russian population of the Zaabramov part of the city and four villages on the Left Bank: Bekereva, Bolshaya and Malaya Rogalikha and Berkulskaya (Tyukova).
In 1887, the Holy Cross Parish Women’s School was opened. In 1897, a new school building was built. In 1901, 61 girls studied at the school. In 1908, 204 girls attended the school.
In the early 1930s in Tobolsk there was a wave of demands "from the workers" for the closure of religious buildings. From the list of closed churches of the city (based on the minutes of the Presidium of the City Council No. 54, § 5 of February 15, 1930 and the minutes of the meeting of the presidium of the district executive committee (OKRIKA) No. 93) in early 1930, the fact of the closure of 16 churches was stated.
After the closure, the temple became a dormitory. In the mid-1950s, they tried to deprive the church of crosses. There was an accident — a worker was killed by a broken cable. In 1965, the church turned into the Base of the ORSA Glavtyumenneftegazstroy. For 19 years, the temple was operated as a vegetable storehouse.
At the moment, the temple is mothballed. Its restoration has begun.