In 1892, an epidemic of Asian cholera broke out in Kuban, lasting about 150 days and claiming 15,045 lives. The residents of the region perceived this as punishment for sins and decided that a nationwide prayer would aid in healing. It took place on July 20 in Yekaterinodar at the intersection of Pashkovskaya and Pospolitakinskaya streets. During the service, the townspeople promised to build a church if the disease receded. The epidemic indeed weakened, and on December 21, 1901, the residents turned to the rector of the Military St. Alexander Nevsky Cathedral, Mikhail Voskresensky, asking for help in constructing a chapel in memory of their deliverance from cholera.

The history of the St. Elijah the Prophet Church in Yekaterinodar became known thanks to the research of historian V.P. Bardadym. Sisters Irina and Nastasia Roshchina donated a plot of land for the construction of a house of prayer in honor of the prophet Elijah. On October 26, 1903, a Construction Committee was formed, and on November 2, the foundation stone was laid. The project was developed free of charge by engineer Nikolai Petin.

The complete furnishing of the church was finished in early 1907, and its consecration took place on February 25. Five years later, it was decided to add a bell tower, and fundraising began. However, the wall paintings were never completed due to the events of 1917. In 1918, the church became a parish church, and well-known priests of that time served there.

In 1931, the church was closed, but ten years later, it was reopened by German occupiers, which caused discontent among the Soviet authorities. In 1954, a petition for the demolition of the church was submitted, but it was lost. In 1963, the church was closed again, and for over 25 years it was used as a warehouse.

In the late 1980s, the church was returned to the faithful, and restoration began. On August 2, 1990, the church was consecrated by Archbishop Isidore. In 1993, a brass icon of St. Elijah the Prophet was installed. In 1999, Sergiy Ovchinnikov became the rector, who paid attention to the historical significance of the church as a monument of Cossack culture.