The Church of Saint Blessed Prince Alexander Nevsky in Jerusalem was conceived by the Imperial Orthodox Palestinian Society (IOPS) as a monument to Emperor Alexander III, the founder of the society.

During archaeological research at the Russian site in the old city of Jerusalem from 1861 to 1884, ancient artifacts were discovered, including the Threshold of the Judgment Gate, through which Jesus Christ passed to his execution.

In 1884, the IOPS decided to build a structure over the holy site, initially named the "Russian House," and later renamed the Alexander Courtyard in honor of Emperor Alexander III.

Construction of the courtyard took place from 1887 to 1891 under the guidance of IOPS representatives in Jerusalem, Dmitry Smyshlyaev and N. G. Mikhailov.

The society decided to include a house church in the architectural complex, concealing this from the authorities of the Ottoman Empire and the Patriarch of Jerusalem, Nicodemus, due to its proximity to the Church of the Holy Sepulchre and potential obstacles in obtaining construction permits. Until 1890, information about the church's construction remained a secret, but soon it became impossible to hide due to the building's features.

Tsarevich Nicholas Alexandrovich planned to ask the Sultan for permission to build the church during his visit to the Holy Land. The IOPS prepared for his arrival, completing the construction of the courtyard complex covering 1342 m² with the church still not landscaped. On September 5, 1891, the solemn consecration of the Alexander Courtyard took place, but the church was not yet ready, and the iconostasis awaited the Sultan's permission. Icons by V. F. Paskhin and Nikolai Koshelev depicting the Passion of Christ were placed on the western walls.

The receipt of the Sultan's firman was delayed for another 4 years. In 1894, Alexander III passed away, and Grand Duke Sergei Alexandrovich decided to immortalize his memory by building a church in the name of Saint Alexander Nevsky. After negotiations with Patriarch of Jerusalem Gerasim and Turkish authorities, the issue was resolved by April 1896.

On May 22, 1896, Patriarch Gerasim of Jerusalem consecrated the Church of Alexander Nevsky, assisted by Archimandrite Raphael and numerous clergy. The celebrations were organized with the participation of IOPS representative N. G. Mikhailov, General Russian Consul Alexei Kruglov, and others. At that time, the Easter bells were ringing in the Trinity Cathedral and the Church of the Ascension on the Mount of Olives. IOPS Secretary Vasily Khitrovo instructed N. G. Mikhailov to ensure that a memorial service for the emperor and all mentioned in the Russian House was held every Thursday at the Church of Saint Alexander Nevsky.