Court was first held in the Eagle Hotel, the largest building of the Mission Santa Cruz campus, just south of School Street.

[2] The second courthouse was a building on the east side of present-day Emmett Street nearby.

[3]: 44 Later, the third site for the court was held in the "flatiron edifice" (built by Hugo Hihn in 1860, between present-day Front and Pacific)[2] until a new courthouse, designed by Thomas Beck, was constructed by Sedgewick J. Lynch and George T. Gragg in 1866 for $20,000[4]: 23  and completed in 1867 at Cooper and Pacific.

[2] It was built on land deeded to the county in April 1866; the selection of the "flats" of Santa Cruz rather than the hill on which the mission stood was a matter of some controversy, as a group had already proposed to donate Mission Hill land, which the county accepted, then rescinded once the Cooper Street offer was extended.

[4]: 25–26 As the building aged, multiple replacements for the 1896 courthouse were proposed starting in 1927, and an annex was built to alleviate overcrowding in 1937, then remodeled in 1949.