By the time Conrail took over most railroading in the northeastern United States in 1976, the renamed Port Reading Secondary (terminology used by Conrail to describe branch lines) was little more than a seldom used line that serviced local industries.

This status continued throughout the 1980s and into the 1990s as Conrail saw little need for the redundant Port Reading Secondary beyond providing local freight services (Conrail used the Lehigh Line for most traffic into the New York area from the south).

In 1999, CSX and Norfolk Southern split Conrail, but because of the Port Reading Secondary's proximity to the New York City consumer market, they could not decide how to split it, so, they took most of the lines near NYC and they created a separate company, Conrail Shared Assets Operations.

To respond to the challenge of serving the increased demands of the New York/New Jersey region, CSAO invested millions of dollars to upgrade the Port Reading Secondary to handle long distance trains, including intermodal trains taking an alternate route to their terminals along the Chemical Coast Line, such as NS's E-Rail Terminal and the PANYNJ owned ExpressRail terminals.

Rail traffic has increased substantially on the Port Reading Secondary in recent years as a result of the upgrades.