The Catholic community of St. Joseph's Parish dates back to its founding in 1898. The Catholic elementary school was opened at St. Joseph's Parish in September of 1938 under the direction of the Franciscan Sisters of Alleghany, New York, who led the school until 1987. The school has continued in existence since 1987 under the direction of a lay administration and faculty. Since 1960, St. Joseph's Academy has been a feeder school for Santa Fe Catholic High School. St. Joseph's Academy has also been instrumental in the development of two other parochial schools.

A parochial, coeducational elementary school, St. Joseph's Academy has been fully accredited by the Florida Catholic Conference since 1973. The most recent reaccreditation occurred during the 2010-2011 school year.

Currently, there are approximately 243 students enrolled from Preschool to 8th grade.