The history of the Church of the Holy Apostles Peter and Paul in Karlovy Vary began in the summer of 1862. At the initiative of Grand Duchess Elena Pavlovna, charitable funds were raised for the construction of the church. Many people responded to this call, including representatives of noble families such as Count Shuvalov, Count Koshelev, and Prince Vorontsov. The Karlovy Vary City Council, when the resort was part of Austria, also supported the project by providing a plot on Schlossberg Street, which is now named after Peter the Great.

The church project was developed by architect K. A. Ukhtomsky, but there were not enough funds. Instead of an Orthodox church, an Anglican one was built on the planned site, and for the Russian church, part of a mansion was purchased, where a house church was arranged. This building was the most magnificent at the resort, and the church was consecrated in one of the halls of the Grand Hotel Pupp. However, due to the popularity of Karlovy Vary among Russians, soon there was not enough space.

In June 1893, the first stone of the new church was laid, and four years later it was consecrated. In the early 20th century, a 'Turgenev Fund' appeared at the church, and it was planned to open a 'Russian House' for the convenience of Russian vacationers. However, these plans were thwarted by World War I. The church's rector, Nikolai Ryzhov, was arrested by the Austrian administration and sentenced to death, but thanks to the intervention of King Alfonso XIII, he was pardoned. The church was closed until the end of the war, and the gilding and copper from the domes were removed. Since 1918, after the Bolshevik Revolution, the church has provided shelter for clergymen who escaped from Russia.