With the growth in population in Kingston and with the increased complexity of the law, the 1796 courthouse and jail were deemed to be too small by the mid-19th century. The courthouse and jail were sold and contracts were let for the new courthouse in July 1855 on land obtained from the province.

The new building was to serve the united counties of Frontenac, Lennox and Addington. Limestone for the building was quarried on the site. The first court session was held in November 1858. Construction of a new jail and jailor's residence had started immediately behind the courthouse. After the 1874 fire in the courthouse, it was decided to build a new registry office to the east to relieve the crowded quarters in the courthouse. The courthouse and registry office are associated with 19th-century judicial, governmental and administrative development in Ontario.

The present courthouse was designed by architect Edward Horsey and constructed by builders Scobell and Tossell in a neoclassical style with a bold two-storey front portico with frieze, cornice, Ionic columns, pilasters, coffered ceiling and tympanum with the Royal Coat of Arms, a centre three-storey block and two-storey side wings with pediments, and classical detailing. After the 1874 fire, architect John Power redesigned the central dome on a drum lit by 16 arched windows framed by pilasters and accented by moulded arches and keystones with a top lantern. Cupolas with octagonal drums and ribbed domes on the end pavilions were also added at this time; construction was undertaken by contractor George Newlands. The Registry Office with its hammered-dressed limestone ashlar walls and classical details was built to the provincial design and specifications. An addition was made to the west elevation facing Court Street in 1963. Both the courthouse and registry office sit at the top of a gentle incline overlooking a large city park along the lakefront. An ornate 1903 fountain sits in front of the main entrance to the courthouse. The courthouse remains a Kingston landmark.

In 1975, the City of Kingston designated the courthouse under the Ontario Heritage Act, and in 1980 the structure was designated a National Historic Site. The Ontario Heritage Trust secured a heritage easement on the building in 1989.