Church of Mary Magdalene is located in the Södermalm district. The history of the church dates back to the 1350-th year, when King Magnus Eriksson with the approval of Pope Clement VI built a chapel and dedicated it to Mary Magdalene. The external appearance of the building of those years badly documented, and only extant copper engraving depicts the chapel as a small building with a large tower, topped with a pointed spire.

At the beginning of the 1520s freed Gustav Vasa in Stockholm, and his troops headed by Peder Fredagom camped in the chapel, but they suffered heavy losses when the Danish army of Christian II attacked them from the city. This event may have been one of the main reasons why Gustav Vasa destroy all churches, monasteries and chapels that surround the city, after the introduction of Protestantism in 1527, including the Chapel of Mary Magdalene. However, his son, King John III, began the construction of a new church on the site of the chapel in 1588. However, his death in 1592 interrupted the ongoing construction work, and the church remained unfinished until 1634.

Architects Nicodemus Tessin the Elder and Tessin Jr. took over the continued construction and built the baroque church. The spire, which was considered the most beautiful in Stockholm, was destroyed during a fire in 1759 that also destroyed 300 other buildings in the area. Carl Johan Cronstedt was commissioned to restore the church, and his project was completed in 1763. It has retained much of the original design. Restoration of the interior of the Church of Mary Magdalene was held in 1927, the same year there was established the first body, a second was added in 1986.