Saint Mark School first opened its doors on September 24, 1924, founded as a parish school by Monsignor Daniel J. McCarthy. The school was placed under the care of the Sisters of St. Dominic of Columbus, Ohio, who guided its early years. Located in Sheepshead Bay, Brooklyn, Saint Mark quickly became a cornerstone of the community, providing a strong faith-based Roman Catholic education to children of primarily Irish and Italian immigrant families. Just four years later, in 1928, the school proudly graduated its first class of 13 students.

In the years following World War II and continuing through the 1970s, the academy experienced tremendous growth, reaching its highest enrollment in 1975, when 135 students graduated. Throughout these decades, the school remained deeply committed to serving the children of the parish. The Sisters of St. Dominic continued their dedicated service for nearly sixty years, with the Dominican Sisters of Amityville becoming an integral part of the teaching community in the early 1950s.

As the neighborhood changed during the 1980s and 1990s, so did the school. The student body became more diverse, welcoming children not only from the parish but also from nearby communities such as Brighton Beach and Coney Island. At the same time, the faculty transitioned from being predominantly religious sisters to a dedicated team of lay educators.

For its first four decades, Saint Mark School was tuition-free, with all expenses covered by the parish. Beginning in the mid-1960s, families began paying tuition, and since then the school has sustained itself without relying on parish subsidies. When Father Joseph Grimaldi became pastor in 2000, the school faced financial challenges and was close to requiring diocesan support. Through his leadership and the guidance of the Finance Committee, Saint Mark regained stability and financial health.

In 2015, the school entered a new chapter, officially becoming Saint Mark Catholic Academy. Today, under the leadership of Father Robert Mucci and a dedicated lay board of trustees, the academy continues to thrive with an enrollment of 340–350 students and 19 full-time faculty members. For more than a century, Saint Mark Catholic Academy has remained true to its mission of nurturing faith, fostering learning, and preparing young people for bright futures.