In 1970, Penn Central declared bankruptcy, the largest in American history at the time. In 1971, Amtrak took over intercity passenger operations, ending the long-standing Baltimore-Harrisburg-Buffalo passenger service. The following year 1972, Tropical Storm Agnes caused severe damage to the NCR's right-of-way and bridges. In 1972 Penn Central filed for abandonment of the destroyed section between Cockeysville, MD, and the Mason-Dixon Line, but through the efforts of the Stewartstown Railroad, the northern portion was saved. In 1973 the Pennsylvania Department of Transportation purchased the right-of-way from the Mason-Dixon Line north to York. In 1975 the ICC approved the abandonment of the section from Cockeysville, MD, to the PA state line. Rail was removed from that section in late 1975 and early 1976.
The Stewartstown Railroad proposed the formation of the York County Southern Railroad, which led to the creation of the Southern York County Corporation. In 1976, Conrail was formed from bankrupt northeastern railroads. In 1976 the Maryland & Pennsylvania Railroad became the designated operator. Lease agreements and rebuilding contracts followed, and in January 14, 1985 the Stewartstown Railroad operated the first train over the reopened section. Passenger excursions began, and in 1988, PRR K4s #1361 visited York for celebration of 150 years of railroading. In 1990, the Pennsylvania Department of Transportation sold the line to York County.
The 1990s saw the development of the York County Rail Trail. In 1992 rail service was terminated by the Stewartstown Railroad. In 1996, the Liberty Limited Dinner Train began operations, and in 1998, the original New Freedom passenger station was demolished for a replica to be built. In the 1999, the Rail-Trail was completed. In December of 1999, Emons Transportation Group merged the Maryland & Pennsylvania Railroad with YorkRail into the York Railway Company, the New Freedom passenger station was completed, and in 2001, the Liberty Limited Dinner Train made its last run.
March 2023 saw the completion of the renovation of an ex-Northern Pacific caboose, enhancing the excursion experience. Also in March 2023, Jody Anderson Leighty made history as the fifth generation in her family to lead a railroad, taking the helm as president of NCR. June 2023 was a time for celebration as the NCR marked its 10th anniversary, a testament to its enduring appeal. October 2023 Ashley Zimmerman was appointed executive director. December 2023 saw the addition of two heavyweight coaches, nicknamed the Trail Sisters, to the fleet. August 2024, Jennifer Kreig became Superintendent Operations Manager, the first female to hold that position at NCR.
September 2024, the board made the difficult decision to remove #17 from service to begin a rebuild for its 1472 inspection, signing a contract with the Strasburg Railroad. That same month, the NCR acquired GE 80-ton diesel locomotive #34, which had its first operational day on September 28, 2024. Finally, November 2024, #17 departed for the Strasburg Railroad to begin its rebuild.
