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Dedication services for the new school were held on the evening of September 2, 1946, with His Excellency Most Reverend Bishop M.S. Garriga officiating. Classes began the following day with an enrollment of 114 students from grades one to seven. A kindergarten was established in 1958. With the opening of an Air Force Base in Harlingen, the addition of more classrooms became imperative; therefore, the former Episcopal Church building was purchased by the parish and dedicated to the exclusive use of the primary department. Five new classrooms were constructed during the period between June1960 and November 1960 on Van Buren Street across from the rectory. On November 4th, the kindergarten, first and second grades were moved to this building and their classrooms were then occupied by the third and fourth graders. Enrollment continued to grow until it reached a peak of 476 in 1961-1962. Due to the closing of the air base, enrollment began to decline. Eighth grade was discontinued in 1967-1968 and the seventh grade was discontinued the following year. This was due to decreased enrollment and the hardship involved in meeting Texas Education Agency Accreditation Standards when the Catholic Dioceses of Texas decided to seek blanket accreditation in 1969.
From 1968 to 1985, Saint Anthony Catholic School included kindergarten through sixth grades. In 1984, an Extended Day Program was added, and in 1985 a pre-kindergarten was added, both of which are still in operation today. During the fall of 2003, Saint Anthony Catholic School opened a Middle School in conjunction with Immaculate Heart of Mary Church. Saint Anthony Catholic School now provides a quality Catholic education for pre-kindergarten through eighth grade students in the Harlingen area.