In the 17th century, Noginsk was known as the yamskoye village of Rogozha, where the current cathedral stands on the site of the church of St. Nicholas. In 1755 and 1767, parishioners built a stone church in Rogozha, known as Old Rogozhsky Yam, in honor of the Epiphany of the Lord with an altar dedicated to St. Nicholas the Wonderworker. In 1782, the village became a town and was named Bogorodsk.

In 1822 and 1824, a refectory was added to the church with altars in honor of the Protection of the Mother of God, in memory of the city's liberation from the French in 1812, coinciding with the feast of the Protection, and St. Nicholas. At that time, a two-tiered bell tower was also built. In 1873, the church became a cathedral, which was soon dismantled at the request of the parishioners, and in 1876, a new, more spacious church was erected in honor of the Holy Epiphany of the Lord with the same altars. In 1885 and 1886, the bell tower was raised with a third tier, and in 1890, a bell weighing 1250 poods, the largest in the district towns of Russia, was installed, cast from donations from the townspeople. In total, there were 13 bells.

The cathedral owned a stone chapel in the churchyard with more than 90 icons, a stone two-story house next to the cathedral built in 1834, a stone chapel in the city square erected in memory of the salvation of the royal family on October 17, 1888, a stone two-story house on Shosseynaya Street with a shop and a wooden wing, a wooden single-story building on church land, and a wooden watchman's house built in 1896.

Since 1895, the future hieromartyr Konstantin Bogorodsky, archpriest Konstantin Alexeyevich Golubev, was appointed as the rector. His relics were discovered on November 20, 1995, and are now located in the Tikhvin Church of Noginsk Bogorodsk.

Later, the rector of the cathedral became archpriest Nikolai Alexandrovich Speransky, who was arrested and exiled in 1931, returned from exile in the mid-1930s, but was arrested again in 1937 and shot in Butovo. Many clergy and active parishioners of the cathedral met the same fate. During the difficult period for the Church, the rector was hieromartyr Sergey Konstantinovich Makhaev, who was also shot in Butovo, followed by hieromartyr Nikolai Alexandrovich Andreev, shot on December 10 in Butovo.

The cathedral was closed in 1938, and from 1940, the building housed a boot production facility associated with toxic substances and a gas distribution station. In 1953, the Noginsk executive committee attempted to destroy the domes and dismantle the bell tower, but the cathedral was preserved.

In 1989, the church was returned to the believers. An important event was the service at the relics of St. Seraphim of Sarov in August 1991. In 1993, the cathedral was seized by schismatics, but in November 1997, it was returned to the Russian Orthodox Church. The first service in the returned church took place on the day of the discovery of the relics of hieromartyr Konstantin on November 20. Gradually, parish life was restored, renovations were carried out, and new carved iconostases with painted icons were installed.

Chaplains are attributed to the cathedral in honor of the Tikhvin Icon of the Mother of God on the cathedral grounds, in memory of those who fell in the Great Patriotic War in Victory Square, and a chapel in the city cemetery.