It was established as Scouting Squadron 31 in 1942, based at Naval Air Station Squantum, Massachusetts.

It flew the dive bombers Douglas SBD-5 Dauntless, then the Curtiss SB2C-4E Helldiver in the North Atlantic until disestablished at the end of the war in 1945.

In 1990 the squadron participated in "Operation Desert Shield", arriving in the Red Sea within a few days of the invasion of Kuwait.

VS-31 deployed for Washington's maiden cruise and then again for the carrier's first Mediterranean Sea deployment in May 1994 where she took part in the 50th anniversary commemoration of the D-Day invasion and Operation Deny Flight.

In 1998, the squadron was deployed aboard the John C. Stennis (CVN-74) on its maiden voyage, during which it spent 131 days in the Persian Gulf supporting "Operation Southern Watch".