The Cathedral of the Epiphany was founded in 1693 behind the eastern wall of the Irkutsk Kremlin. Initially, it was wooden and called the Peter and Paul Church, like one of the towers of the Kremlin. All the buildings of the temple burned down in the fire of 1716.

Two years later, it was decided to restore the cathedral, but already from brick. The funds for its construction were donated by the residents and guests of Irkutsk. Six years after the laying of the first stone, the Peter and Paul Chapel was built in honor of the holy apostles Peter and Paul.

In 1729, the construction of the bell tower was completed, and on July 22 of the same year, the chapel in the name of John the Warrior was consecrated, which existed until 1818.

During the earthquake on June 27, 1742, the cross on one of the small domes of the cathedral was damaged, and the stone tent of the bell tower collapsed, which was replaced with a wooden dome topped with a spire.

The solemn consecration of the Epiphany Cathedral took place on September 25, 1746.

In 1755, the construction of a stone fence around the temple began. In the 1760s, three more chapels were added to the three-altar cathedral: one on the south side, in honor of the Kazan Icon of the Mother of God, and two on the north side, in honor of John the Baptist and All Saints.

In 1771, the saint Sofroniy of Irkutsk was buried in the cathedral.

On the night of April 23-24, 1804, an earthquake occurred, resulting in the fall of the cathedral's cross and damage to the fifth dome, which was later removed.

In September 1812, the construction of the second cathedral bell tower began. A bell, cast in 1797 weighing over 12 tons, hung on posts and was the largest in the city, receiving the name Big. On March 30, 1815, it was raised to the new bell tower in the style of Russian classicism, which was covered with iron and crowned with a cross on June 10.

On December 30 and 31, 1861, during an earthquake on Baikal, the cathedral again suffered serious damage: the vaults cracked, some arches burst, frames fell out, and two columns in the Peter and Paul iconostasis shifted.

In the second half of the 19th century, the Archiepiscopal residence was built next to the cathedral, where the archbishop's quarters and administrative offices were located. Over time, the Spiritual Consistory was moved here, a library of Orthodox periodicals appeared, and a building for the spiritual school was constructed. There was also a burial place for several Irkutsk archbishops.

In 1894, the construction of the Kazan Cathedral was completed, to which the Irkutsk diocese's cathedra was transferred, which meant the loss of the cathedral's status as a cathedral.

After the October Revolution of 1917, the Epiphany Cathedral was closed to believers. A confectionery workshop of the bakery was placed in its building, and the temple was repeatedly rebuilt for production needs. The square of the cathedral building was divided into several floors for a dormitory.

In 1960, the demolition of the Epiphany Cathedral and the Church of the Savior was planned. Architect Galina Oranskaya from Moscow came to sign the documents. However, instead of demolition, she engaged in reconstruction. At that time, the temple received the status of a monument of architecture of republican significance. The tented bell tower, destroyed by the earthquake in the 18th century, was restored to its presumed original appearance; the project was developed by Oranskaya herself, using preserved analogs in the Moscow region.

In 1968, the bakery's ovens were dismantled, and the restoration of the cathedral began, lasting 18 years. After the restoration, the temple was handed over to the Regional Local History Museum.

In 1994, the Epiphany Cathedral was transferred to the Irkutsk diocese, which soon began to hold services in the Peter and Paul Chapel.

In 2002, the painting of the altar was completed.