St. Mary's German Catholic Church was opened in 1858. In 1864, the Sisters of St. Francis were asked to take over the existing girls school in St. Mary's parish. In 1876, they moved into a new building, located on the South side of Maryland St., west of Delaware St. (current site of Conseco Fieldhouse?).

In the 1940's, St. Mary's Academy was the only private secondary school in Indianapolis that would accept blacks.

The school was closed in 1977, with most of the students moving to Bishop Chatard High School.