In 2005, the Norfolk Southern Railway rebuilt all eight GP40TC locomotives at its Juniata Shops in Altoona, Pennsylvania.

In 1987, New Jersey Transit and Metro-North ordered a set of GP40 locomotives called GP40FH-2s, which were completed by Morrison Knudsen between 1987 and 1990.

A total of 21 units of this type were built; 15 were delivered to New Jersey Transit, and the remaining six were for Metro-North.

Seven NJT units were purchased by Iowa Pacific Holdings and three of those were designated for use on the Hoosier State between Chicago and Indianapolis before Amtrak took over operations again on January 30, 2017.

The HEP motor was removed, unlit number boards were drilled in, the rear ladders were removed and replaced with steps, and LED markers were applied to the rear end of the locomotive, replacing their original tri-color class lights.

In December 2017, New Jersey Transit purchased 17 additional ALP-45DPs to replace the remaining GP40PH-2B locomotives that are still in service.

[4] However, in July 2020, NJ Transit decided to use the ALP-45As to replace older locomotives of the PL42AC fleet instead of the GP40PH-2Bs, due to the PL42AC's unreliability and inability to be upgraded to meet new Environmental Protection Agency standards.

[5] In 2019, NJ Transit unveiled locomotive 4109 painted in a heritage scheme based on that of the CNJ GP40P.

[6] In October 2022, NJ Transit unveiled locomotive 4101 painted in a heritage NJDOT scheme.

[citation needed] The remaining units have been rebuilt by MotivePower into MP32PH-Q locomotives for use on SunRail[11] or sold to various leasing firms.

The rebuild included an EMD 645 prime mover, producing 3,000 hp (2,200 kW), and a separate head-end power (HEP) generator.

[16][failed verification] The Massachusetts Bay Transportation Authority currently owns and operates a set of 25 GP40 passenger diesels known as GP40MCs, used on the MBTA Commuter Rail system.

Currently, the GP40MCs are undergoing an overhaul by the Norfolk Southern Railway, which includes repair and modification to the major propulsion systems and the HEP generators.