In 1992, the Department of Engineering and Environmental Management was created to house the Graduate Engineering and Environment Management Program, which had migrated from the AFIT Civil Engineering School. Six years later, separate programs from AFIT's two graduate schools were consolidated into the Department of Systems and Engineering Management. In 2003, the department established the Environmental Engineering and Science program and the NSA 4012 Information Security program. A year later, the Research and Development Management program was established along with the Operational Technology certificate program.
The Acquisition program was moved to NPS in 2005, while the Industrial Hygiene program was transferred from the Uniformed Services University of the Health Sciences to AFIT in 2006. The Strategic Leadership program was then phased out and the department graduated the last class of these students in 2007. That same year, though, Graduate Financial Analysis was established as a new degree program. In 2008, the Graduate Systems Engineering program was moved from the Department of Aeronautics and Astronautics into the Department of Systems and Engineering Management.
In 2011, a department restructuring was implemented known as the Program Realignment And Consolidation (PRAC). The PRAC was intended to synthesize multiple, disparate department programs into the three thrust areas
The following year, the department established the Systems Engineering Research & Analysis Group (SERAG) to provide a cohesive linkage of academic theory and practical implementation of systems engineering tools and techniques across these thrust areas. In addition, in order to better capture its new structure, the department implemented a name change in 2013, moving the "and" in the title after "Engineering" thus becoming the Department of Systems Engineering and Management.