The station was built in 1830 at the end of the Oliver Viaduct, of local stone (Ellicott City Granodiorite) provided by one of the quarries owned by the Ellicott family, which had founded the town and local flour mill in 1772.

[5] The railroad's inaugural trip from Baltimore to Ellicott's Mills has held on May 22, 1830, with horse-drawn rail cars.

[6]: 27 The B&O demonstrated its first locomotive, the Tom Thumb, at Ellicott's Mills in a famous race against a horse later in 1830.

It was also meant to help the city compete against regional rival Washington, D.C., where construction was starting on the Chesapeake and Ohio Canal.

[9] The B&O Ellicott City Station Museum includes: An HO-gauge model train layout is housed in the 1885 freight house; the layout depicts "the original 13 miles of commercial rail track stretching from Baltimore to Ellicott Mills",[8] and train videos are projected onto the wall behind.

Other static displays include memorabilia explaining the role of the B&O Railroad and the station in the American Civil War.