The Mormon Battalion arrived in San Diego in January of 1847 to support the U.S. military garrison in the pueblo during the war with Mexico. When not engaged in military duties, the Mormon soldiers assisted the community by building new brick-lined wells, laying out walkways, and building the first fired-brick structure in San Diego.

Originally designed as a town hall, the 16'x27' brick building stood on the corner of the plaza facing San Diego Avenue. It had a moderately sloped roof, and the brick walls were whitewashed. Mexican and U.S. members of the Boundary Commission used the building as their headquarters in 1849.

On March 27, 1850, the state legislature incorporated the town of San Diego. From that time until 1869, the building served as the city and county courthouse. It was also used as a meeting place, church, school, and polling place during elections.

The courthouse was destroyed in the 1872 fire. The First San Diego Courthouse Association reconstructed it in 1992 and oversees its operation.

Some reports of the paranormal at this location include the back offices and the jail cell that sits behind the building. In the offices, some have reported seeing the manikin of "Charles Krug" move by itself, and strange footsteps have been heard and lights have been seen around the jail cell at night. There have also been footsteps heard as if someone was walking through the building on occasion as well, yet nobody is seen.