CRMSE opened its doors in 1986 as a research center where SDSU faculty and students could collaborate on research, teaching, learning, and curriculum development. From the vision of Ed Silver with the support of Donald Short, the Dean of the College of Sciences at San Diego State University, CRMSE started as one room within the math department. By the end of the 1986/87 academic year, the center moved to its current space on Alvarado Road. Additional founding members included: Nicholas Branca, Fred Goldberg, Elsa Feher, Sandy Marshall, Doug McLeod, Judy Sowder, and Larry Sowder.
By 1987, the College of Education joined CRMSE in an effort to bring together the campus, students and community in a new way. CRMSE became the place on campus to come together and collaborate across multiple disciplines, particularly math and science. Original members included: Nadine Bezuk, Cheryl Mason, and Alan McCormack.
Within a few years after it was established, CRMSE faculty, together with faculty from the UCSD Colleges of Biological and Physical Sciences, partnered to develop a plan for a joint doctoral program in Mathematics and Science Education (MSED), which was approved by the California State University and University of California systems in 1993.