The museum is devoted to the history of naval aviation, including that of the United States Navy, the United States Marine Corps, and the United States Coast Guard. Its mission is "to select, collect, preserve and display" appropriate memorabilia representative of the development, growth and historic heritage of United States Naval Aviation. More than 150 aircraft and spacecraft are on display, including four former Blue Angels A-4 Skyhawks, the Curtiss NC-4 (the first aircraft to cross the Atlantic), U. S. Coast Guard helicopters, biplanes, a K-47 Airship control gondola and tail fin, an aircraft that President George H. W. Bush trained in, and the S-3 Viking used to transport President George W. Bush to the USS Abraham Lincoln in 2003 (see Navy One). These historic and one-of-a-kind aircraft are displayed both inside the Museum's 300,000 square feet of exhibit space and outside on the Museum's 37-acre grounds. The museum also functions in coordination with the Naval Air Systems Command (NAVAIRSYSCOM or NAVAIR) as the Navy's program manager for nearly all other retired Navy, Marine Corps and Coast Guard aircraft on display aboard U.S. military installations in the United States or overseas, or in numerous other museums or public displays. In a similar manner to U.S. Air Force aircraft on loan from the NMUSAF's collection which remain under official USAF ownership, these other American-preserved naval aircraft continue to remain the property of the Department of the Navy and are typically identified at these locations as being "On Loan from the National Naval Aviation Museum."

In addition to the displays, the museum features a Giant Screen Theater, flight simulators, Blue Angels 4D Experience, museum store, and cafe. The Cubi Point Café is itself an exhibit as it displays squadron memorabilia from the closed NAS Cubi Point Officers' Club.