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CEU was established in 1907 by pedagogists Librada Avelino and Carmen de Luna as the Centro Escolar de Señoritas, based in Parañaque. Its main purpose was to teach "ideal womanhood, intelligent citizenry, and democratic leadership that would instill in the tenets of science and virtue." At the time of its establishment, it was the first non-sectarian women's educational institution in the Philippines (now a coeducational educational institution). It founded the College of Pharmacy in 1921, pioneering medical education in the Philippines. Subsequently, the Colleges of Liberal Arts, Education, Business, Dentistry, and Optometry were also established one after another. It began operating as a university in 1930 and in 1932 was converted into a corporation for financial reasons. Its name was then changed to Centro Escolar University, which still holds today. In 2009, the School of Law and Jurisprudence was established.

There is also an Integrated School at CEU, which was established upon the university's founding. It was removed from the Mendiola campus in the mid-1990s and in Malolos in 2004 after nearly 100 years open. It was revived starting in the 2014-2015 academic year as the Centro Escolar Integrated School (CEIS) and is offered in Manila, Malolos, and Makati.

There have been seven presidents in the history of CEU: Librada Avelino (1907-1934); Carmen de Luna (1934-1962); Pilar Hidalgo-Lim (1962-1972); Dionisio Tiongco (1972-1992); Lourdes Talagechauz (1992-2002); Rosita L. Navarro (2002-2006); and Cristina Padolina (2006-present).