In 1846, Orthodoxy arrived in one of the oldest cities in Estonia, Viljandi, previously known as Fellin. By the decree of the Holy Synod, an Orthodox parish was established here, and the following year, a wooden church was built, consecrated in honor of the Prophet, Forerunner, and Baptizer of the Lord, John. The church was constructed from rough hewn beams, was small, and was located in a marshy area.

In 1960, the old wooden church was dismantled, and the parish was temporarily given the sacristy of the Jan Lutheran Church. However, over time, the sacristy became dilapidated, and major repairs were planned for the Jan Church. Metropolitan Alexius of Tallinn and Estonia appointed Archpriest Vyacheslav Seliverstov as acting rector and tasked him with finding a new location for the parish.

The city authorities offered the building of a former morgue. Architect Aili Liik from Tallinn, who was not Orthodox, developed the renovation project for free, following the instructions of Father Vyacheslav. All internal partitions were demolished, the windows were elongated, an altar apse and a small porch were added, and a small dome was placed on the roof. Inside, an iconostasis, kiots, and an elegant tomb from the closed church were installed. The building acquired a true church appearance and seemed as if it had adorned this place for a long time. In 1998, the church was consecrated by Archbishop Cornelius.