In the early 20th century, a small chapel stood on the site of the modern St. Nicholas Church, built even before the construction of the famous Slyudyanka railway station. Traditionally, when a significant settlement or station appeared, a chapel, and sometimes a church, was built first.

Grand Duke Nikolai Alexandrovich, the future Emperor Nicholas II, visited Slyudyanka on his way to Irkutsk after returning from a round-the-world trip from Japan. It is said that he suggested an avenue lined with trees leading from the station gates to the church, so that everyone could enter the church and thank God for the safe completion of their journey. This was recounted by Archpriest Vladimir Sharunov, the former rector of the Slyudyanka church, who passed away in May 2004. It was decided to relocate an already completed church from the ravine "Polovinka" of the Circum-Baikal Railway, where it had been erected in 1903. Initially, it was planned to set it up at the Malyy Baranchik station, but ultimately the rapidly growing settlement of Slyudyanka was chosen. The church was moved in early 1906 and consecrated the same year by Priest Innocenty Churinov from the neighboring Kultuk church, as there was no priest appointed in Slyudyanka yet.

The clerical records of the Kultuk Nicholas church for 1907 describe the church building as wooden, one-story with a bell tower. The church had one altar in the name of St. Nicholas, St. Innocent, and Martyr Tatiana. The church was heated by one stove, and there was a lack of utensils. The clergy consisted of one priest and a psalmist, who lived in a railway house. Until 1907, they did not receive a salary from the treasury, but from January 1, they were assigned a salary from the Trans-Baikal Railway: 1200 rubles per year for the priest and 720 rubles for the psalmist. Priest Nikolai Mustafin, the son of an official, was ordained in 1906, and the psalmist was Vladimir Makov. The church elder was Vasily Toroptsov.

By 1914, the parish of the St. Nicholas Church had over 500 households and about two thousand parishioners. The church was attended as needed, but everyone tried to come for Sunday and holiday services. Since the old church could not accommodate all who wished, it was decided to dismantle it and build a new one.

The new building was erected by workers constructing the second track of the Circum-Baikal Railway. 2000 rubles were allocated from the state treasury for construction and 3250 rubles according to the estimate from the Ministry of Railways. Church income and donations from parishioners were also used. In the new church, as in the first, there was one altar in the name of St. Nicholas the Wonderworker, St. Innocent of Irkutsk, and Martyr Tatiana.

The church was built in pseudo-Russian forms with elements of Russian modernism, resembling a small tower with tents and kokoshniks. The building was wooden, one-story, with a foundation and plinth made of Baikal marble. The walls were made of logs, and the plinth and frieze were covered with boards. The church had a cross shape, with two doors leading to marble porches. The altar had two windows and two extensions, likely for the sacristy and vestry. The main entrance was from the western marble porch with a tented canopy.

The narthex was divided into three parts: a room with a staircase to the bell tower, a room for the watchman, and a passage to the church. Heating was provided by five stoves. Above the narthex rose the bell tower with a tented top and a dome with a cross. A square structure with a tent and dome was arranged above the roof of the central part. Four small domes rose at the corners of the roof, as well as above two finials on either side of the bell tower and above the tented canopy. The church project was developed by the Orthodox German Gunther. The church was built next to the station and represented the face of the station. An avenue lined with acacias led from the church doors to the station, and trees from the old taiga remained around.

According to the memories of Vladimir Bykov, the road near the station and the passages around the church were paved with cobblestones from the shores of Baikal. The street, named "Second Station Street," was built up with shops and stalls. Other locals also spoke of the stone pavement. The church fence was made of cast iron, but its fate is unknown. The new church was consecrated on December 29, 1915.

The rector of the new church became Mikhail Boldovsky, who held this position since 1911 after graduating from the Irkutsk Theological Seminary.

In 1922, church valuables were confiscated from the Slyudyanka church: two silver vessels, an altar cross, a censer, and three icon vestments weighing a total of 10 pounds and 36 zolotniks of silver.

The St. Nicholas Church was closed in 1929, but in 1947 the building was returned to the faithful, and services resumed on April 27 of the same year. The church building has now been restored to its original appearance.