The Morristown Line is the core of the Morris & Essex Lines service, as the timetables that include it and the Gladstone Branch are labeled. It is the core of commuter rail service running on the former Lackawanna main line. Until the Montclair Connection opened on September 30, 2002 combining the Montclair Branch with the Boonton Line, the Montclair Branch up to Bay Street was also included in the Morris & Essex Lines timetables and most trains are still (except for not showing intermediate stops) included to show connections at Newark Broad Street for travelers to change trains to go to Hoboken or Secaucus Junction and New York-Penn Station and between Denville and Hackettstown. The line is electrified between Dover (electrification reached Dover in 1931) and Hoboken and New York Penn Station, with infrequent diesel service shared with the Montclair-Boonton Line continuing to Hackettstown on Weekdays only.

Historically, all Morristown Line service only operated to the ex-Lackawanna terminal in Hoboken. New Jersey Transit opened the Kearny Connection on June 10, 1996 that allows electric Morristown Line trains to cross over onto the Northeast Corridor and enter New York-Penn Station, these trains are named MidTOWN DIRECT trains. Today base service on the line is hourly electric trains running from Dover to New York-Penn Station. During weekdays, these trains skip Mountain Station, Highland Avenue, and East Orange, that are served by Gladstone branch trains running to and from Hoboken about 10 minutes later. During rush hours additional trains operate, including some trains between only New York-Penn Station or Hoboken and Summit. Diesel trains on the line are less frequent and run weekdays only with 6 trains per day between Hackettstown (a few start/end at Mount Olive or Lake Hopatcong) and Hoboken, most making most local stops and connecting with MidTOWN Direct trains in Dover, additional peak hour service between Dover and Hackettstown is provided by Montclair-Boonton Line trains.

On weekends train service runs hourly with MidTOWN DIRECT trains operating between Dover and New York-Penn Station. These trains make all stops except for alternating between serving Mountain Station and Highland Avenue (these stops only get service every 2 hours on weekends), these trains connect with Gladstone Branch Shuttle trains running on the Gladstone Branch in Summit, and Montclair Branch (replicating the pre-2002 service on this branch) service to Hoboken running to and from Montclair-Bay Street.

For rolling stock all MidTOWN DIRECT trains use ALP-46 electric locomotives that can change voltage on the fly because there is a voltage change at the Kearny Connection, these cars operate in push-pull mode with BiLevel cars or single-level Comet coaches, with only Comet V coaches now used as cab cars because they have the PTC equipment. Trains running west of Dover use generally single-level Comet cars and a diesel locomotive. The few electric trains between Dover or Summit and Hoboken during rush hours can also use Arrow III MU cars.