All of the class were equipped with the Pennsylvania Railroad's cab signal system needed to operate into Penn Station; Washington, D.C.-Boston through trains over the Hell Gate Bridge, plus the Montrealer/Washingtonian, were their main assignment throughout their New Haven careers.

The units were known as "Jets" due to the roaring sound made by their main blowers; an example of this characteristic was inadvertently preserved for posterity in a scene shot at Grand Central Terminal, the very first moments of the movie The Man in the Gray Flannel Suit.

However, the class also had a tendency to overheat and catch fire due to the crowded, poorly ventilated internal component arrangement, a situation made necessary by the need for the units to conform to the weight restrictions imposed by the New York Central's Park Avenue steel viaduct.

This problem was significantly aggravated by the New Haven management's de-emphasis of electric operations in favor of its new dual-power FL9 diesels, and the railroad's financial condition.

The E-40s continued in this service, steadily dwindling in number, until May 1973 when the Metropolitan Transportation Authority suddenly banned them after #4971 caught fire in the Park Avenue Tunnel; all went into dead storage.