The Bay Town Trolley provides public bus transportation. The trolley route includes major shopping centers, hospitals and transportation to Panama City Beach. Southern Greyhound provides intercity bus transportation.

Northwest Florida Beaches International Airport (ECP) is one of the newest airports in the United States. Located only minutes from Downtown Panama City, ECP is one of the most popular transportation choices for travelers. The airport services flights from American Airlines, Delta Air Lines, Southwest Airlines and United Airlines. ECP offers more than 650 one-stop destinations and international connections in Atlanta, Austin, Baltimore, Charlotte, Chicago, Dallas, Denver, Houston, Nashville, and St. Louis.

The following car rental agencies are located either at the Airport or in convenient locations near the Airport: AAA, Alamo, Avis Budget, Cartempts USA, Dollar Enterprise, Hertz, National, Sears and U-Save. Several taxi and limousine services offer ground transportation from the Airport.

The Bay Line Railroad provides rail freight service to Panama City businesses and industry and to Port Panama City. "The Bay Line" interconnects with both the CSX Transportation Company in Dothan, Alabama and in Cottondale, Florida. "The Bay Line" also interconnects with the Norfolk Southern Railroad in Dothan, Alabama.