The origins of the New Jersey Museum of Transportation began with the purchase of a Baldwin 0-4-0T engine from the Raritan River Sand Company in 1952 by a pair of railroad enthusiasts.

Initially a 2.5-acre (1.0 ha) plot of land on Route 9 in Marlboro was purchased where the railroad was run as a tourist attraction, but in 1952 when the organization was facing large property tax increases the not-for-profit Pine Creek Railroad Division of the New Jersey Museum of Transportation was formed and the operations were moved to its present-day location in Allaire State Park.

[3] Buildings on the grounds include the Allenwood Station (built by the Pennsylvania Railroad in the early 1940s for use in Allenwood, NJ), the Freneau Station (built by the Jersey Central in the early 1900s on the CNJ Freehold Branch), a Union Newsstand (built circa 1910 in Manasquan, NJ, purchased in 1969), a crossing shanty, a maintenance shop, a heavy equipment building, a car barn (used for storage of rolling stock), as well as an office (Raritan River Railroad #7).

After viewing several digital images it was discovered, through the evidence of several artifacts on the engines, that they were Civil War-era Patentee Class 2-2-2T[a] locomotives from between 1850 and 1855.

[17][18] On September 25, 2004, the New Jersey Museum of Transportation was granted custody of the two engines by U.S. District Judge Joseph Irenas.