[3] The three lines each bought a one-third share in the Junction Railroad on August 1, 1861, and the company was organized on October 3.

From West Philadelphia south to Grays Ferry, the Junction Railroad mostly paralleled the WC&P, and had to cross it somewhere, leading to a dispute between the two companies and a delay in opening the southern half.

The Reading began operating passenger trains over the entire Junction Railroad on September 3, 1873, with a transfer to the PW&B at Grays Ferry.

[11] On April 1, 1876, the Reading leased the northern piece of the line for a year to access a temporary station for U.S. centennial celebrations.

[citation needed] The PRR's West Philadelphia Elevated line, completed in 1904, provided an alternate route for freight trains that would use the central piece of the Junction Railroad through the Market Street Tunnel or the PRR's River Line along the Schuylkill.