A new schedule will take effect Sunday that reflects rail operations system wide of 99.6 percent with 697 out of 700 trains that were running before Sandy.
The agency says it will offset the three remaining trains with increased service on lines based on ridership.
The changes include six additional trains on the Morris & Essex Lines and six trains add on the Montclair-Boonton Lines.
Midtown Direct service along the Gladstone Branch will use double-decker rail cars.
The Pennsauken Transit Center will open on Monday, which will provide a first-ever direct connection between River Line light rail service and the Atlantic City Rail Line.