On August 7, 1948, VF-3A became the VF-31 Tomcatters. The original VF-31, "The Flying Meataxes" destroyed 165 Japanese planes in aerial combat, tops among all CVL (light carrier) squadrons. They deployed with USS Cabot, CVL-28, from November, 1943 through September 1944.

The Tomcatters’ combat experience includes battles in World War II, Korea, and Vietnam, as well as regional conflicts all over the world. In 1972, flying the F-4J Phantom, Tomcatter aircrew shot down a MiG-21 over North Vietnam and distinguished VF-31 as the only Navy fighter squadron to achieve aerial victories in three wars. Through the years the Tomcatters and their predecessors have served on some of the Navy’s finest aircraft carriers, including the first, USS Langley (CV-1); the second, USS Lexington (CV-2); and the sixth, USS Enterprise (CV-6). They were aboard USS Enterprise during the bombing of Pearl Harbor as well as the Battles of Wake Island, Marcus Island, Midway, Guadalcanal, and the Eastern Solomons. In 1980, VF-31 and USS Saratoga (CV-60) concluded a 24-year period of continuous service together, the longest in naval history.

The Tomcatters currently fly the most capable and formidable strike fighter in the U.S. Navy, the F-14D Super Tomcat. Ten fighter/reconnaissance aircraft constitutes VF-31. Each Tomcat can track up to 24 targets simultaneously and attack six with Phoenix missiles while continuing to scan airspace. The F-14D has a new capability: It can strike with precision air-to-ground weapons using the Low-Altitude Navigation and Targeting Infrared and Night (LANTIRN) targeting system.

From 1952 to 1957, VF-31 flew the F2H Banshee. In 1957, the squadron switched to the F3H Demon, flying it through 1962. For two years after this the Tomcatters flew the F-3B before transitioning to the F-4B Phantom. After two years with the B model, the squadron switched to the F-4J, and flew this through 1981. Then in 1982 the Tomcatters began flying the F-14A Tomcat. VF-31 flew the F-14A for ten years before switching to its current aircraft, the F-14D Super Tomcat, in 1992.

CDR James R. Barnett, commanding officer of Fighter Squadron 31 (VF 31), was temporarily relieved of command, 21 February 1995 pending completion of an investigation into the 13 January 1995 mishap in which two F-14D "Super Tomcats" from the Miramar-based squadron collided in mid-air. The F-14D "Super Tomcats" were on a routine training mission off the coast of San Diego when the collision occurred.

In late 1996 VF-31 returned from its second Western Pacific deployment aboard USS Carl Vinson (CVN-70), flying missions in the Arabian Gulf and over southern Iraq in support of Operations Southern Watch and Desert Strike. Following cruise the Tomcatters returned to NAS Oceana, where they resided five years earlier before moving to NAS Miramar. The squadron remains part of Carrier Air Wing 14 on the west coast, and returned from a deployment aboard USS Abraham Lincoln (CVN-72) in December 1998, again in support of Operation Southern Watch