The roots of the NAWCTSD reach back to April 1941 when then-Commander Luis de Florez became head of the new Special Devices Desk in the Engineering Division of the Navy’s Bureau of Aeronautics. De Florez championed the use of "synthetic training devices" and urged the Navy to undertake development of such devices to increase readiness. In June, the desk became the Special Devices Section.

Throughout World War II, the Section developed numerous innovative training devices including ones that used motion pictures to train aircraft gunners, a device to train precision bombing, and a kit with which to build model terrains to facilitate operational planning in the field.

The Special Devices Section grew and became the Special Devices Division. In August 1946, the Division, at its newest home at Port Washington, Long Island, NY, was commissioned the Special Devices Center.

As NAWCTSD evolved and grew, it was aligned at various times under several different parent organizations within the Navy. In 1956, it became the Naval Training Device Center. Over a three-year period in the mid-1960s, the Center moved from its Long Island location to Orlando, Florida, taking residence as a tenant activity at the then-Orlando Air Force Base, that installation subsequently becoming Naval Training Center Orlando in 1968 until its closure by Base Realignment and Closure (BRAC) action in 1999.

In 1985, the then-Naval Training Equipment Center became the Naval Training Systems Center. In 1988, the Center moved to its present headquarters, the main building complex named for its founding father, de Florez. On October 1, 1993, the Naval Training Systems Center became today’s NAWCTSD. In 2003, the command was briefly renamed Naval Air Systems Command Training Systems Division (NAVAIR-TSD), but has since reverted back to its original name. In 2005, the physical facility and property was also designated as NSA Orlando. NAWCTSD remains a significant component of the Naval Air Systems Command.