The Far Rockaway branch is the Long Island Railroad’s second-lowest ridership electric branch to operate with all day hourly or better service. The branch runs for 5 miles from the end of Atlantic Branch at Valley Stream and is entirely double-tracked at street level with many grade-crossings. After Valley Stream all off-peak service continues the 16 miles along the Atlantic Branch to Atlantic Terminal, making the total trip length of most trains 21 miles from Atlantic Terminal to the Far Rockaway LIRR Station. During rush hours service also operates to and from Penn Station. Late night service runs to and from Jamaica on weeknights, with shuttle service to and from Valley Stream during early Saturday and Sunday Mornings.

Far Rockaway Branch trains originally continued to Rockaway Park along the line now used by the IND Rockaway Line, today these tracks are used by A Subway Trains to Far Rockaway, and S Rockaway Park trains (running via the now not normally used in regular service track at Hammels wye). LIRR service was discontinued in 1955 to allow the conversion of the LIRR tracks to become part of the Subway System, with Subway service extended to the Rockaways on June 26, 1956. Travel times from Far Rockaway to Atlantic Terminal are as fast as 51 minutes via the LIRR, and 55 minutes via the A train (from the nearby Hoyt-Schermerhorn Station to Mott Avenue). Penn Station (on a peak one-seat ride train) travel times are as fast 53 minutes, but the A train takes 67 minutes. Prices though are only $2.75 for the subway, but nearly 5 times the amount $12.50 peak/$9.25 off-peak for the LIRR (as of June 2021) to Atlantic Terminal or Penn Station. Promotional fares that reduce travel costs within New York City like CityTicket and Atlantic Ticket are not valid to and from Far Rockaway since the journey goes via Nassau County. Although LIRR Far Rockaway branch service was basically unaffected by Superstorm Sandy (returned in just a few weeks instead of 7 months) there were zero attempts to offer discounted fares to commuters that had to rely on shuttle buses between Far Rockaway and Howard Beach-JFK Airport to connect with the subway.