More than 150 aircraft and spacecraft fill the museum's exhibit halls and outdoor grounds. The collection spans the full arc of naval aviation history, from early canvas-and-wood biplanes to Cold War-era jets. There is the training aircraft that a young George H. W. Bush flew before becoming the Navy's youngest pilot at age 18 during World War II. There is the S-3 Viking that carried President George W. Bush to the USS Abraham Lincoln in 2003 - designated "Navy One" for the occasion. The control gondola and tail fin of K-class blimp K-47 recall the Navy's lighter-than-air patrol missions. Coast Guard helicopters document the service's rescue heritage. Each aircraft carries a story: where it flew, who flew it, and what it meant to the sailors and Marines who depended on it.

The Emil Buehler Naval Aviation Library, established in 1992, serves as the museum's research heart. Named for aviation pioneer Emil Buehler, whose philanthropic trust funded its creation, the library holds about 400,000 photographs along with books, oral histories, manuscripts, and technical manuals. Its special collections include records from the Brown Shoe Project, which compiled stories from aviation squadrons that flew during the Korean War. Buzz Aldrin's flight training records from his early Navy career are preserved here - the paperwork of a future moonwalker, filed alongside thousands of other young naval aviators who learned to fly over Pensacola Bay. The library hosted the 50th anniversary commemoration of the Apollo 11 Moon landing in 2019, connecting Pensacola's training mission to the furthest reaches of human flight.

Most Tuesday and Wednesday mornings from March through November, the roar of F/A-18 engines shakes the museum walls. The United States Navy Flight Demonstration Squadron - the Blue Angels - is based at NAS Pensacola, and the museum grounds offer a front-row seat to their practice demonstrations. The team's connection to the museum runs deep. Captain Robert L. Rasmussen, a former Blue Angels demonstration pilot and Navy fighter pilot, served as museum director for 27 years before retiring in 2014. The Naval Aviation Museum Foundation, a 501(c)(3) nonprofit, has raised tens of millions of dollars since 1966 to build exhibits, recover and restore aircraft, and develop educational programs. Adjacent to the museum, the National Flight Academy houses over 30 networked flight simulators inside a four-story simulated aircraft carrier, hosting more than 200 students per week during summer programs.

The museum's recent history has been turbulent. In September 2004, Hurricane Ivan damaged the building and several aircraft on outdoor display. Then in December 2019, a gunman killed three people and injured eight more at NAS Pensacola, prompting the closure of the museum and other attractions to the general public. The COVID-19 pandemic kept doors shut for seven additional months in 2020. For three and a half years, the world's largest naval aviation museum sat largely inaccessible. On May 17, 2023, the museum finally reopened to the public, with visitors now required to show valid state-issued identification. A new exhibit on naval aerospace medicine opened in October 2024, a reminder that the collection continues to grow. The museum began in a cramped World War II-era building in 1962. Six decades later, it endures as a testament to the generations of aviators who first took flight from these Florida shores.