The SD50 since it was first produced has been a troubled locomotive. A finicky electrical system combined with engine failures and excessive vibration doomed it from the start. However NS starting in 2008 embarked on a program to upgrade these tired locomotives to extend their service lives, thus the SD40E was born.

The Juniata rebuild turned "bad actor" SD50 into some of the most reliable locomotives on the railroad.

The SD40E is a complete rebuild utilizing either new or remanufactured parts. These include a rebuilt 16-645 prime mover, EM2000 microprocessors, new electrical, and a refurbished (A/C'd) cab. The first SD40E emerged in November 2008. The first 30 units are equpped with Helper Link for service on the Pittsburgh Line. The balance are used in ballast and work train service.