The Port Washington Branch is the only Long Island Rail Road Branch not to pass through Jamaica and have connections to other branches, instead it branches off the Main Line just after Woodside and runs 15.1 of its own independent miles, 20 minutes travel time total to Great Neck and Port Washington on the north shore of Nassau County. The electrified branch provides service to 9 stations in Queens and only 4 in Nassau County. The branch is double tracked for its first 14 miles until just beyond Great Neck, before becoming single-tracked the remaining 4 miles to Port Washington. It has only one grade-crossing, at the Little Neck Station, which is the only grade-crossing in all of New York City still used by passenger trains (since the one remaining rush hour train to use the Lower Montauk branch between Jamaica and Long Island City was eliminated in 2012), this grade-crossing (the rest are on slow service freight lines) is also by far the most dangerous one in New York City.

All trains run to and from Penn Station generally half-hourly or better throughout the day to Port Washington. During rush hours some service terminates and originates at Great Neck, with poor reverse peak service to and from Port Washington, Manhasset and Plandome caused by the single-track nature of the end of the branch. After the 2009 recission service was reduced to hourly headways at off peak hours on weekdays and on weekends in September 2010 (this schedule has also been used today due to reduced ridership caused by the COVID-19 pandemic), these service changes were reversed on weekdays in 2012, and weekends on November 16, 2013. These changes in frequency caused a large dip in ridership on the branch that is still recovering.