The Pensacola and Atlantic Railroad was chartered on March 4, 1881 to connect Pensacola with the parts of Florida east of the Apalachicola River, straight across the sparsely-populated Panhandle. The railroad company completed its surveys and began full construction on June 1, 1881. Official ground breaking ceremonies in Pensacola on August 22, 1881 brought into focus the importance of the West Florida enterprise and its evident relationship with the expanding Louisville and Nashville Railroad. The Louisville and Nashville Railroad L&N was operating the original Alabama and Florida Railroad and subsequent Pensacola Railroad route into Pensacola from Flomaton Alabama, forty-four miles to the north.

The Pensacola and Atlantic Railroad was constructed in less than two years' time with different sections of the railroad being built simultaneously by different contractors. The first Pensacola and Atlantic locomotive arrived in Milton in May 1882 by water and was placed in work train service constructing the railroad eastward from Milton. The first train over the newly constructed Escambia Bay Bridge arrived on August 15, 1882.

Upon completion of the Apalachicola River bridge west of Chattahoochee in February 1883, the river crossing at Sampson's landing was abandoned. Service from Pensacola to Jacksonville, Florida began the first week in May 1883 via connections with the Florida Central and Western Railroad, later Seaboard Air Line Railroad, at River Junction, Florida. Milton Depot

The Pensacola and Atlantic Railroad received financial backing from the Louisville and Nashville Railroad during construction and ceased operating as an independent line on July 1, 1885 when it was incorporated into the Louisville and Nashville system. Ninety seven years later in 1982, the Louisville and Nashville Railroad merged with the Seaboard Coast Line Railroad, Atlanta and West Point Railroad, Georgia Railroad, Western Railway of Alabama, and Clinchfield Railroad to form the Seaboard System Railroad. In 1985, the Seaboard system and the Chessie system merged to form CSXT Rail System.

When the Pensacola and Atlantic was constructed through Northwest Florida in 1881-1883 the Florida panhandle was sparsely populated. The only two areas that warranted a depot were Milton and Marianna, Florida. Other depots were quickly added as people moved in to settle the wild lands and traffic began to increase. There were sixteen depots built in the first years.

Passenger service peaked in the 1920's with six trains a day calling at Milton. With the coming of the automobile and airplanes that were heavily subsidized by the government, diner interior passenger service started going into the red. Four trains survived until 1967 when the Louisville and Nashville along with other railroads lost the mail contracts.

The remnant of the streamliner "Gulf Wind", inaugurated in 1949 to replace steam-powered heavy-weight cars, survived until Amtrak's formation.  Its last run was on April 30, 1971.

The Gulf Wind's final years saw just token service consisting of one engine, one baggage car, one coach, and one sleeper with a diner between Jacksonville and Chattahoochee only. The service had been reduced to three times a week in an attempt by the Louisville and Nashville and the Seaboard Coast Line Railroad to cut costs and to help support the discontinuance petition filed with the ICC. diner

The Museum also commemorates the service to Northwest Florida of the St. Louis-San Francisco Railway, known as the Frisco.  The Frisco started service to Pensacola in 1927 after buying earlier logging railroads and extending a line from Amory, Mississippi.  Through service was provided to Memphis, the Midwest, and the west coast by the "Sunnyland" passenger trains and Frisco's famous "Fast Freight" trains.  The last passenger service to Pensacola was in 1955, and the passenger depot on the corner of Garden and Coyle streets was razed in the 1960's. frisco engine on garden street

A Frisco freight locomotive was donated to the city of Pensacola and rests in the median of Garden Street in front of the old depot site.  Freight service to Pensacola continues through the Burlington Northern, which purchased the Frisco in 1980.  The track south of Flomaton, Alabama is now owned by the Alabama and Gulf Coast Railway.

Beginning on April 4, 1993 Amtrak's "Sunset Limited" provided through service across frisco engine displayNorthwest Florida from Los Angeles, California to Miami, Florida via New Orleans, Louisiana, and Jacksonville, Florida with stops at Pensacola and Crestview. The "Sunset Limited" ended a twenty-two year hiatus in passenger service across the Florida Panhandle.

In August 2005 Hurricane Katrina destroyed the main line along the Louisiana and Mississippi Gulf Coast thus ending Amtrak's "Sunset Limited" and passenger service in North West Florida.