On June 6, 1905, a meeting was held at the Shilka station to discuss the need for building a church, selecting a location, and financing. An oversight committee was established at this meeting to monitor donations and verify reports on the church's construction. A procedure for convening meetings of the donor committee members was also set. At that time, there was already a church in the village of Mitrofanovo in honor of Saint Nicholas, which was attended by the residents of Shilka. However, with the development of the station and the growth of the population, there arose a need for a church of their own, as most of Shilka's residents were railway workers with shift work, making it difficult to attend the church in Mitrofanovo.

On June 29, Father Iakov Znamenksy of the Mitrofanovo Nicholas Church, along with Father Mikhail Plyaskin of the Gorodishchensky Church and Deacon Nikolai Znamenksy, conducted the laying of the church at the Shilka station in the name of Saints Peter and Paul, with about 1,000 worshippers present. Iakov Znamenksy suggested that those present lay a stone in the foundation of the church.

By 1908, with funds from railway parishioners, the church was built and consecrated by Bishop Mephodiy of Transbaikalia and Nerchinsk on March 30, 1908. The church building was wooden with a bell tower, covered with roofing iron, and had three gilded domes. In early 1909, an independent parish was formed at the Shilka railway church. On April 7, 1909, Father Nikolai Pavlovich Vinogradov was appointed as the rector of the Peter and Paul Church. Until June 1909, the church belonged to the second deanery of railway churches, and on June 24, 1909, it was transferred to the 25th deanery of the Transbaikal and Nerchinsk diocese. The lower chapel of the church was laid with hewn stone and filled with earth, creating the impression that the upper chapel stands on a hill. The upper chapel was constructed from timber in the village of Kibasovo and was moved to its current location three years later. Thanks to the efforts of railway workers and local residents, this church in honor of Saints Peter and Paul was established. The pre-revolutionary church staff included five clergymen: a protodeacon, two priests, a deacon, and a psalmist.

In 1929, the church was closed and soon used as a transit prison, primarily for priests and so-called kulaks. After the prison, the building housed a forge, a vocational school, a vegetable storage facility, and a grain warehouse, then a gym and a museum. Only in 1990 did a local deputy help gather and formalize a community of believers. After that, lengthy efforts began to evict former residents. The gym was removed, but the museum remained in the basement, and progress for the parishioners was slow.

The building was handed over to the believers in a deplorable state: the ceiling was like a sieve, the windows were boarded up, the walls were bent, the heating system was absent, and there were no domes, crosses, icons, or church utensils. In 2002, a fundraising campaign for bells was announced, and in a year and a half, enough money was raised to purchase six bells, the largest of which weighs 7 poods.

Currently, a Sunday school and a refectory operate at the church, providing meals not only for the church's novices but also for many low-income individuals. A charitable hotel for five guests is available for pilgrims.