With the successors to the GP28 and GP35, the more powerful variant with 3,000 hp was again offered as the GP40. The major innovation of this generation was the introduction of the new EMD 645 engine, which had 645 cubic inches or 10.6 liters per cylinder. To accommodate the new engine, the locomotive's frame and hoods were lengthened by three feet. These locomotives could also be recognized visually by the three fans of the same size on the rear part of the hood. Between 1965 and 1971, in the USA and Canada a total of 1,187 units were built for US customers, 16 units for the Canadian National and 18 units for two Mexican railway companies. The Norfolk & Western Railway was the only customer to make use of the option of having a driver's desk installed in each direction of travel. Some engines were built as GP40P and GP40TC for operation in front of passenger trains. These were longer to accommodate the train heating.

The GP38 was offered as a less powerful variant from 1966, which achieved an output of 2,000 hp without a turbocharger. It was also an economic success with 706 units, six of which were delivered to Mexican customers. Derived from the GP38 was the GP38AC, which had an AC generator. In the years 1970 and 1971, a total of 21 units went to the Canadian Pacific and 240 to US customers.

In the meantime, the GP39 had emerged, which was powered by a smaller engine with twelve cylinders and a turbocharger. It produced 2,300 hp and was therefore slightly above the GP38. Only 23 of them were built, and the Burlington Northern later had some GP30s and GP35s converted to GP39s.