The SD45 had already been offered optionally as the variant SDP45 with steam heating for use in front of passenger trains. When the ATSF was looking for new locomotives for their prestige trains Super Chief and El Capitan, the performance data of the SDP45 was actually suitable for the task. However, the ATSF was bothered by the optics, since the narrow body with running boards were generally associated with freight locomotives and therefore did not meet the requirements. A new passenger locomotive was now required with a body that occupies the entire width of the vehicle and with a powerful 20-cylinder prime mover. In order to reduce the development costs given the small quantities to be expected, EMD developed the FP45 with load-bearing frame and a non-bearing body.

The ATSF ordered nine engines, another five units without dynamic brakes were delivered to the Milwaukee Road. The locomotives were not long used by either operator for passenger trains, as Amtrak was founded in 1971 and both stopped passenger services. On the Milwaukee Road, the FP45s were only repainted and used technically unchanged in freight train service. That's why they were scrapped in the early 1980s. The ATSF's engines were repainted from the familiar Warbonnet livery to other liveries, but at the same time the steam generators were removed and the gearing was adjusted for a top speed of 89 mph. They were used, among other roles, for the “Super C”, which was a special fast freight train for transporting containers and semi-trailers. In the 1980s all but one were modernized, getting the designation SDFP45 and the electronics of the SD45-2, and the top speed was again reduced to 83 mph. A few years later there was a further reduction to 71 mph. They were retired in the late 1990s after merging with the Burlington Northern. 

After the delivery of the nine FP45, the ATSF immediately ordered 40 freight locomotives, which were to have the same powerplant and body. The body promised better aerodynamics in order to achieve better performance with fast-moving freight trains. Half of the locomotives were fitted with steam lines so that they could be used behind a locomotive with a steam generator in front of passenger trains if required. The Great Northern ordered 14 engines, hoping to provide better cold weather protection for crews compared to other locomotives with open running boards. Mpre engines were ordered by the Burlington Northern. In the course of time, many locomotives were rebuilt, so the engines of the ATSF were converted in a similar way to the SDP45. Many examples changed hands over time and remained in use until shortly after the turn of the millennium.