St. Francis Xavier Catholic School was established in 1939, under the leadership of Rev. Msgr. Joseph E. Buckley, pastor of St. Francis Xavier Church. On March 4, 1940, Baltimore Archbishop Michael J. Curley officially dedicated the school. St. Francis Xavier students were taught by the Sisters of Notre Dame under the leadership of Principal Sister M. Anastasia, S.N.D. In the early years, St. Francis Catholic School had an enrollment of 382 students. The first graduation, with a class of 57 students, took place in 1942.

When the school was first built, Anacostia was a rural community. The newly constructed Sousa Bridge brought an influx of new homes and families to the area. In conjunction with the population explosion, the enrollment in the school blossomed to over 1,000 students, and the school opened a second building in 1954 to support the growing numbers. The opening of additional parishes and schools in the area to compensate for the population growth, however, and movement of parishioners to the suburbs, led to the school leveling off to approximately 200 students today.

Ms. Teresa Leeke became the first lay principal in the early 1990s. In 1997, St. Francis Xavier Catholic School joined the Center City Consortium as part of a group of inner city schools, organized by James Cardinal Hickey of the Archdiocese of Washington. With seventh and eighth graders studying Latin as well as Spanish and all students from first through eighth grade participating in St. Jude’s annual Math-a-Thon, our academic standards continue to be high. In the Fall of 2008, the Consortium was restructured, and St. Francis Xavier Catholic School became St. Francis Xavier Catholic Academy.