From Thanksgiving through the New Year, local model railroad groups set up large layouts on the roundhouse floor and in select locations on the grounds of the museum.

In 2021, the museum's Mount Clare Station building was designated as a National Park Service Underground Railroad Network to Freedom site.

The inaugural horse-drawn B&O train traveled the 13 miles (21 km) of the newly completed track from Mount Clare to Ellicott Mills (now Ellicott City, Maryland), on May 22, 1830, the first regular railroad passenger service in the U.S.[6] The existing Mount Clare station brick structure was constructed in 1851.

In 1990, CSX deeded the property and collection to the newly formed, not-for-profit museum organization governed by an independent board of directors and provided it with a $5 million endowment.

[13] In the early morning of February 17, 2003, heavy snow from the Presidents' Day Storm collapsed half of the roof of the museum's roundhouse.

Reporting on the devastation the following day, The Baltimore Sun said, "...hours after the collapse, columns of mangled steel stuck out from the roundhouse ... Locomotives and passenger cars in the museum's collection, some dating from the 1830s, could be seen covered with snow and debris.

"[3] The roundhouse, with a newly repaired roof, reopened to the public on November 13, 2004, and the damaged locomotives and cars were surrounded by a plexiglass barrier.

The museum's rolling stock collection include both originals and replicas, some of which were built by the B&O for its centennial "Fair of the Iron Horse" in 1927.