The first parish school for grades 1 to 8 was open from 1964 to 1972, but closed due to staffing and financial difficulties. For the next twenty years, the building functioned as a parish center, CCD office and classrooms and location of the Shoreline Soup Kitchen.
Through the support of the parish and diocese, Saint John School officially reopened in August 1994, for grades Pre-K through 8.
In 1999, a new wing was added to the school, which is now the lower grade classrooms. The science lab was modernized in 2002-2003, and the library was relocated and improved in 2004-2005. The gymnasium/auditorium/cafeteria was renovated in 2007. New windows and an energy efficient heating/cooling system were installed in 2011-12. The roof of the middle school wing was replaced in 2013.
Saint John School celebrated its 20th Anniversary with special events during the 2013-2014 school year. In summer 2015, the exterior campus of the school was re-designed & upgraded. Improvements included re-paved parking lots, new sidewalks, landscaping & lighting. 2017 saw the replacement of the gymnasium roof, followed in 2018 by the addition of energy efficient lighting. In Summer 2019, the gymnasium doors were replaced.