The Museum occupies the L&N Milton combination freight and passenger depot that was built in 1907-09 on the site of the original 1882 P&A depot. The station was closed in 1973, bought by the Santa Rosa Historical Society, and partially restored with a 1976 Bicentennial grant. The Museum moved into the building in 1989 and completed the restoration. Its car displays include L&N Dining Car 2722, Globe Coffee House, L&N Dining Car 2715, a former Pullman sleeper car, renovated into L&N baggage-dormitory car 1652, L&N caboose 1148, Frisco caboose 1102, L&N box car 18050 and L&N flat car 21107. Outbuildings include a bridge tenders house from the Escambia Bay trestle and a section shed with motor car. The Museum houses a wide variety of memorabilia from the L&N, Frisco, and other railroads.

The Museum operates a gift shop in the restored main waiting rooms of the depot which stocks a variety of model railroad kits and supplies, primarily N and HO scale, and also a number of gift souvenir items. Model supplies which are not stocked can be special ordered with short delivery time if the items are available at suppliers. The gift shop carries several books on local railroad history. Museum members receive a discount on all gift shop purchases.