The Singapore Armed Forces Football Club (SAFFC) originated from the Singapore Armed Forces Sports Association (SAFSA) Football Team. The latter participated in all FAS-sanctioned tournaments, including the National Football League (NFL) since 1975. During this time, SAFSA had among its ranks, outstanding footballers such as Hussein Aljunied, Dollah Kassim, Quah Kim Song, Lim Tien Jit, Muniandy Kumar, Seak Poh Leong, Lim Chiew Peng, Leong Kok Fann, Au-Yeong Pak Kuan, Malek Awab, V. Selvaraj, Salim Moin and Terry Pathmanathan. The objective of SAFSA was to provide opportunities for full-time National Servicemen and Regulars to contribute to the development of football in Singapore.

When the S.League was incepted in 1996, SAFSA pulled out from the National Football League (NFL), an amateur competition, to enable the formation of the SAF Football Club. The Club was officially established on 16th February 1996 as the Singapore Armed Forces Football Club. The Home Stadium allotted to SAFFC was Jurong Stadium, located at Fourth Chin Bee Road Singapore 619697.

However, in 1999, SAFSA resumed participation in the NFL competition. This was to enable more talented football players enlisted for NS to continue maintaining their standards even though they were not selected to play for SAFFC in the S.League.

On 7th of February 2001, the Club moved to its current premises in Choa Chu Kang stadium, 1 Choa Chu Kang Street 53, Singapore 689236.

SAF FC was organized and structured on a professional framework under the S.League structure. Today, the team comprises of foreigners, local professionals, Full-time National Servicemen and students.