In 1756, a small Roman Catholic boys' school was opened in Frederick, Maryland, which provided a space for class and mass to be held.

In 1822, subscriptions were being taken and construction of the boys school had begun on East Second Street (in the eastern section of downtown Frederick) by August 7, 1828.

With attendance expanding, the original school structure built on Second Street by founder Father John McElroy in 1828 was demolished and a new building was erected in its place in the eastern sections of downtown Frederick.

Embarking upon its new goal of moving from the historic "Prospect Hall" mansion property, by whose name it had been known by for almost 45 years, the School began a "re-branding" campaign and changed its title to "Saint John's Catholic Prep".

On Monday, December 5, 2011, Saint John's agreed to buy the former St. Thomas More Academy property in Buckeystown for an undisclosed amount.

[7] With its holdings now encompassing the original St. Thomas More buildings, and with the construction of more classrooms and sports fields, Saint John's Catholic Prep moved from Prospect Hall to the Buckeystown campus in January 2013.

Classes there officially began January 14, 2013, with the school ready to continue its 184-year-old tradition of academic excellence in western Maryland.