[4] Founded in 1960, ITM began life as the Indiana Museum of Transportation and Communication (IMOTAC) with an initial focus on preserving interurbans and trolleys along with early passenger and freight equipment.

[7] In May 1966, IMOTAC operated a series of sesquicentennial excursions from Noblesville to Indianapolis with Grand Trunk Western 5629.

[14] In 1986, the Fair Train equipment was moved back to Noblesville and plans to operate FairTrain '86 were scrapped due to high insurance costs.

From 1988 to 1998, ITM ran several mainline excursions with NKP 587 and its two Milwaukee Road EMD F7's (numbers 83A and 96C) painted in Monon Railroad colors.

In 1990, ITM began operating excursions over the Nickel Plate Railroad line from Tipton to Indianapolis.

In the 1990s, the museum and its equipment were used in film and television, including the Discovery Channel show Rediscovering America, Going All the Way (1997), and 587: The Great Train Robbery (2000).

[20][21][22] In 1999, following the electrical failure of Chicago Transit Authority EL car #4293, ITM shifted away from trolley operations.

In 2008, ITM began offering caboose train rides from the museum site to downtown Noblesville.

The caboose train was initially supposed to be a temporary replacement for the trolley rides with EL car #4293, which was in need of a $50,000 restoration.

With ongoing issues with the city of Noblesville, ITM looked to move the museum to Logansport, Indiana.

[25] During this time, the museum also operated Polar Bear Express excursions over Hoosier Southern Railroad trackage from Tell City, Indiana, to Troy, Indiana, using leased Iowa Pacific Holdings and Hoosier Southern Railroad equipment throughout the fall and winter of 2018.

The deal to purchase the Logansport & Eel River Railroad fell through and ITM was evicted from the LER property.

[3] While located in Noblesville, the Indiana Transportation Museum operated excursion trains on 38 miles (61 km) of a former Nickel Plate Road line originally built for the Indianapolis and Peru Railroad and, at the time of ITM's eviction, owned by the Hoosier Heritage Port Authority (HHPA), which is made up of the Indiana cities of Indianapolis, Fishers, and Noblesville.

While the museum was in Noblesville, it had in its collection the 1898 private railcar of Henry Morrison Flagler's Florida East Coast Railroad (FEC) #90.

At the beginning of 2003, the museum's operating steam locomotive, Nickel Plate 587, was taken out of service for a federally mandated boiler rebuild.

[34] As of 2025, the locomotive is to be auctioned off by the Kentucky Steam Heritage Corporation due to unpaid storage fees.

[35] While in Noblesville, the Indiana Transportation Museum operated different excursions, ranging from holiday trains to shuttles in freight cabooses.