In August 1990, Metropolitan Pitirim (Nechaev) of Volokolamsk and Yurievsk blessed the site for the construction of a church in honor of the Resurrection of Christ in Yuzhno-Sakhalinsk. The construction progressed slowly. The cathedral's design was developed by architect S. M. Michenko, inspired by the architecture of Novgorod. The regional administration and the mayor of the city, I. P. Farkhutdinov, provided significant support for the construction.

On February 23, 1993, the Yuzhno-Sakhalinsk and Kuril Diocese was established, and the church under construction became its main cathedral.

On January 7, 1995, on the feast of the Nativity of Christ, the first service was held in the new church, although work on the interior decoration, exterior finishing, and landscaping was still ongoing. The Resurrection Cathedral became the first fully-fledged Orthodox church in the region, as previously parishes were located in converted buildings.

On September 11, 2002, the construction of the cathedral's bell tower began, consecrated by Bishop Daniel. The updated cathedral acquired a new appearance: spacious choirs for archbishop singers were added, the area of the refectory and narthex increased, and a bell tower with a golden dome was built. On October 12, 2003, after the completion of the bell tower and the reconstruction of the building, the new altar was consecrated under the guidance of Bishop Daniel of Yuzhno-Sakhalinsk and Kuril. The solemn service with a procession held that day marked the culmination of the first ten years of the diocese.

On August 20, 2003, the governor of Sakhalin Oblast, Igor Farkhutdinov, and fourteen other regional leaders died in an aviation disaster. At the initiative of Bishop Daniel, a memorial monument with a cross was erected next to the Resurrection Cathedral.

In 2005, an Armenian khachkar, crafted by masters from the Ararat Valley from Armenian tuff, was installed on the cathedral grounds.

In 2007, the construction of a Spiritual Enlightenment Center began on the cathedral grounds, which was planned to include a lecture hall, Sunday school, Orthodox library, and other facilities. The construction was completed in November 2009, and the center was opened on March 3, 2010.