In 1996, the first steps were taken towards the construction of the cathedral. Thanks to the support of Governor Igor Farhutdinov, the Yuzhno-Sakhalinsk City Hall allocated a plot of land for the Yuzhno-Sakhalinsk and Kuril Diocese for the design of the cathedral complex. However, construction was delayed for several years.

In the fall of 2003, the first phase of preparatory work began. By the fall of 2004, it was decided to build a wooden church in honor of St. Nicholas, Archbishop of Myra in Lycia the Wonderworker. On December 19, the feast day of St. Nicholas, a prayer service was held and the construction was blessed, marking the beginning of a new parish.

The church was built from wooden beams, with the missing part provided by Tymovsk Forest Industry Enterprises as charitable assistance.

On April 1, 2005, the first Divine Liturgy took place in the unfinished church.

By the second half of April, the main construction work was completed, and a priest was appointed to the church.

Regular services and rituals began to be held in the church, and the community grew and strengthened. The interior of the church continued to be arranged: a two-tiered iconostasis, left and right choirs, and wooden carvings were made and installed.

In 2005, a Sunday school began operating in the church, and that same year, construction of a separate building for it started.

In 2008, the church received as a gift the icons of the Royal Martyrs and the icon of the Most Holy Theotokos "Sovereign."

On July 22, 2009, the parish of St. Nicholas, Archbishop of Myra in Lycia, was officially registered.

Today, the St. Nicholas Cathedral plays an important role in the life of the parishioners and the entire city. Regular worship services are held here. The priests and parishioners care for local disabled individuals and the elderly, visiting schools, hospitals, and the nearby military unit.

The church grounds are well-maintained: there is a bell tower, a small park with a fountain, and a playground where parents come with their children. The wooden church in traditional Russian style adorns the city and is a local landmark.