In late June 1877, seven Sisters of Mercy set sail from New Orleans, Louisiana, to visit Pensacola, preparatory to the opening of a school, as requested by Bishop Quinlan. Plans were finalized and Saint Michael School was officially opened on September 8, 1877.The new school was located on Palafox Street, approximate site of the present downtown walkway between Jefferson and Palafox Streets, and opened with an enrollment of three hundred children. The first class was graduated in 1886.

In 1910, a new St. Michael School was opened on the corner of Chase and Baylen Streets, with classes from first grade through high school. The rectory, located at 19 West Chase Street, was renovated and served as a convent for the Sisters. State accreditation was granted to both high school and elementary schools in 1939, making St. Michael's the first grade school in Florida to be awarded accreditation from the State of Florida. Records are on file beginning with the year 1921. In 1941, St. Michael High School ceased to exist when Catholic High School of Pensacola was founded which later became known as Pensacola Catholic High.

In1961, St. Michael Elementary School was transferred to the present school location and became an interparochial school at that time. The new campus, with six Sisters and two lay teachers provided instruction in grades 1 through 8. The school received its first Florida Catholic Conference accreditation in 1973.

St. Michael School continues to flourish and is a strong, Catholic presence in the Pensacola area. Our culturally diverse student body comes from all parts of Pensacola and neighboring Santa Rosa County yet the school remains a small, supportive community that strives for excellence.