Milwaukee Road ordered 15 six-axle passenger locos in the early 1970's for service on commuter rail routes around Chicago, which were designated F40Cs. EMD used the SDP40F as a base, but replaced the steam boilers with an additional diesel generator for use with new electrically heated passenger cars. The 16-cylinder used here delivered 3,200 hp. Since other railway companies no longer needed six-axle passenger locomotives, the 15 units remained. When Metra was founded in 1984 for passenger transport in the Chicago area, the locomotives became their property. In the years after the turn of the millennium they were replaced by MP36PH.

Since Amtrak only wanted to procure four-axle passenger locomotives in the future and, due to inadequacies in the steam-powered train heating systems, procured a large number of cars with electric heating, the four-axle F40PH was delivered from 1975. The prime mover delivered 3,000 hp and at the same time drove a second generator, which, depending on the series, generated up to 500 or 800 kW to supply the cars. In order for this generator to generate three-phase current at the required frequency, it was necessary for the engine to run constantly at a nominal speed of 893 revolutions per minute. This made them one of the locomotives that made a loud engine noise even when stationary. Later series received an additional diesel generator and some existing locomotives were retrofitted with it so that they could run at low speeds when idling and more power was available for the traction motors. Retrofit machines are designated F40PH-2C or F40PH-CAT depending on whether the alternators are powered by Cummins or Caterpillar engines.

Of the 475 F40PHs built by EMD, Amtrak had received 210 by 1988. 132 of these were created by Amtrak returning the unpopular SDP40F to EMD and using their engines to build an F40PHR. Other important customers included the Illinois Regional Transportation Authority and Canada's Via Rail. Some vehicles had a slanted front instead of the classic hood. Another 31 pieces were made between 1988 and 1998 by Morrison-Knudsen and MotivePower Industries. Many F40PH were also replaced by the MP36PH after the turn of the millennium, but others continued to be used after 2010. Some machines entered freight service and were fitted with a shorter gear ratio for 65 mph.