Since 2003, the museum has operated a heritage railroad over a 2-mile line along the banks of the scenic Fox River to the Jon J. Duerr (formerly Blackhawk[1]) Forest Preserve.

The southern terminus of the railroad is called "Blackhawk" (see photo below and to the right), and this station lies within the heart of the Jon J. Duerr Forest Preserve.

The sole purpose of this line was to transport coal to the nearby Elgin State Mental Hospital, and the railroad was powered by two ancient home-built electric locomotives.

[5] The coal for the metal hospital was brought in by the Illinois Central Railroad via Coleman Siding on the Aurora, Elgin & Fox River Electric line, which is now a point on the museum's mainline.

The last big development to the museum's mainline occurred in 2003 when the line was extended into the Jon J. Duerr Forest Preserve.

[7][8] On Sunday, July 8th, 2018, two boys, aged 11 and 13 broke into the museum's car barn and inflicted almost $150,000 worth of damage on the 8 antique pieces of history stored inside.

The boy had cut his arm on a piece of glass inside the car barn, and the woman called the South Elgin Police thinking that this was suspicious.

[9][10] In Early November of 2024, the Fox River Trolley Museum announced a new plan to extend their current car barn, which was built in 1984, an additional 50 feet.

[12] The museum maintains a collection of 30 antique electric trolleys, railroad cars, and locomotives which range in construction dates from 1887 to 1973.

The majority of the museum collection is focused on railways and electric transit lines of the Chicago area.

[14] The most recent collection acquisitions include the interurban electric railway car, Aurora, Elgin & Fox River Electric Co. #304, that was built for the Fox River Line in 1923, and ran in daily service between Elgin and Aurora until March 1935.

AE&FRE #304 made its first run over its original railroad on August 21, 2010, over 75 years after it last ran on the line.