Aside from the pier, the flight deck is the museum's largest section for events. The outdoor space atop the 29,000-ton vessel houses a collection of restored aircraft, including the MiG-27 jet fighter and the A-12 Blackbird spy plane. The can hold 2,500 guests for concerts, receptions, and seated dinners.

A major part of the venue's overhaul was to upgrade the technology and the structural layout of the Intrepid's main section, the 720-foot-long hangar deck. The Exploreum, one of the hangar deck's halls, was redesigned with events in mind and now has mobile exhibits and a custom drape system (developed by Drape Kings) that can be used to subdivide the space. The renovation also installed a 10- by 30-foot video wall at the entrance, new lighting and projection systems for the 245-seat Allison and Howard Lutnick Theater, and modern displays for the museum's relics.

Additionally, the Intrepid offers classroom space in the Michael Tyler Fisher Center for Education, an area for outdoor cocktails in the Fantail, and presentation equipment in the great hall.

Catering by Restaurant Associates is the museum's exclusive food provider.