Trinity Parish was organized September 18, 1844, at a time when the population of Janesville, Wisconsin was 200. The congregation was the 12th parish to be organized in the then Territory of Wisconsin. The first rector of the parish and the moving force behind its organization, was the Rev. Thomas J. Ruger. The Rev. Ruger served as rector until 1855, when he resigned to become the City of Janesville's first postmaster. Present day "Ruger Avenue" is named after him.

The first services of the parish were held in a small brick school house located on Bluff Street (Parker Drive) on the east side of the River near Milwaukee Street, and continued there until January of 1846. Services were then moved to "The Old Stone Academy" on South High Street on the west side of the river. The Vestry took action on July 5, 1847 to "construct a new church edifice of brick, 42 feet wide by 70 feet long". The church was consecrated in 1848, when the 2nd Convention of the Diocese of Wisconsin took place in Trinity Parish. The new church was located on present day Centerway, just southeast of Robinson's Cleaners.

In 1859, a second parish, Christ Church, was established on the east side of the river. This congregation's church building was located on the present Church grounds. Christ Church remained open only until 1919.

The Rev. Henry Willmann became rector of Trinity Parish on December 6, 1907. The congregation prospered greatly during his rectorship of 25 years. It was under his leadership that Christ Church united with Trinity Parish. The present Trinity church building was constructed in 1930, where Christ Church had stood and was renovated in 1978-79. Ortmayer hall was built in 1964.

Trinity Parish has the distinction of having had the first pipe organ in Janesville (cost $1,000), the first marble altar in the Wisconsin Territory, and the first "vested choir in the West". Trinity was organized in 1844 while Jackson Kemper was Bishop of Wisconsin, after having served as the first Episcopal Missionary Bishop in the Northwest Territory.