A new schedule took effect Sunday that reflects rail operations system wide of 99.6 percent with 697 out of 700 trains that were running before Sandy.
Only three cars will not be back to regular service.
The agency says it is trading out those trains, with increased service on its busiest lines.
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.
The storm caused $450 million in damage to rail cars, tracks and stations.