Conrail acquired the line in 1976, and later sold some of it to the Norfolk Southern Railway to relieve that company's ex-Nickel Plate Road main line. CSX Transportation acquired the entire line in the 1999 breakup of Conrail, and began to make improvements, including new crossing signals, paving crossings, and weeding the railroad. After this was complete, signs were posted at each crossing notifying motorists of an increase in train traffic.
In 2004, operations under the Chicago, Fort Wayne and Eastern Railroad name began; from the beginning of operations, the railroad has been owned by RailAmerica. In 2011 former Norfolk Southern supervisor Joseph (Joe) Parsons was named the General Manager of Chicago, Fort Wayne, & Eastern Railroad headquartered in Fort Wayne, Indiana.
On July 23, 2012, Genesee & Wyoming Inc. announced that it intended to purchase RailAmerica in a deal valued at $1.39 billion. Approval of the purchase was granted by the U.S. Surface Transportation Board on December 19, 2012, and ownership of the Chicago, Fort Wayne and Eastern was transferred to the G&W.