After the visit of the royal family to Yekaterinodar in 1888 and their miraculous escape from a train crash, the idea of building the Cathedral of Catherine emerged. A year later, the city council decided to establish altars in the church in honor of the heavenly patrons of Alexander III's family: St. Alexander Nevsky, St. Mary Magdalene, St. Nicholas the Wonderworker, St. George the Great Martyr, St. Prince Michael of Tver, St. Xenia, and St. Princess Olga. The main altar was dedicated to St. Catherine the Great Martyr, the city's patroness. It took many years to raise funds and prepare for construction. The design of the church was entrusted to the city architect I.K. Malgerb, a graduate of the civil engineering institute, while the engineering calculations were performed by B.K. Pravdzik. By 1898, the project was completed.

Architecturally, the church resembled the cathedral in Novocherkassk: five domes, a bell tower above the main entrance, window decorations, and facade decor. The composition was complemented by two symmetrically located chapels at the main entrance, as well as chapels in the crypt. The church was to become the largest in the Kuban region. The project was approved by the city council, and construction began. The laying of the church took place on April 23, 1900. Construction was delayed due to a lack of funds and political events. General construction work was completed only in 1911, and in September, crosses were installed on the domes. Then, finishing work began, entrusted to the Society of Russian Artists. The frescoes covered key areas of the walls, vaults, and domes, with plans to depict about seventy scenes from the New Testament and saints among 'Byzantine' and 'Old Russian' ornamentation. There were also plans for a richly decorated marble iconostasis. The consecration of the cathedral took place on March 23, 1914, but work on the interior decoration continued for several more years.

After the revolution, the cathedral became Renovationist, but this did not save it from persecution. Church valuables were confiscated, and in 1931, bell ringing was prohibited. Thanks to the efforts of I.K. Malgerb, the cathedral was preserved, but it was closed and used as a warehouse. The cathedral's activities resumed in 1944 after Krasnodar was liberated from the fascists. The names of the chapels were changed to the Assumption, Resurrection, Annunciation, Sergius, and Barbara chapels, while the main chapel retained the name of Catherine. By the 1000th anniversary of the Baptism of Rus, the cathedral's wall paintings and iconostasis were updated. In 1990, the cathedral acquired a bell tower with seven modern bells, and in 1992, the 'Blagovest' bell weighing one and a half tons. The cathedral now has 12 bells.