Weinstein told the (Newark) Star-Ledger his resignation takes effect March 2. He talked to the newspaper at Penn Station in Newark, one of the system's major hubs.
"It's time to move on," he said, "This, the time I served as commissioner, they're almost like gifts. You have the opportunity to serve. I love transportation."
Weinstein was appointed to head NJ Transit by Gov. Chris Christie. He served as state transportation commissioner under the previous Republican governor, Christine Todd Whitman, and is the only person to have held both positions.
NJ Transit is the third largest mass transit agency in the country and the largest to serve an entire state, operating trains, buses and three light rail lines.
The agency increased train fares 25 percent as Weinstein's tenure began, but he promised to avoid future increases for at least three years and did so. Weinstein, a rail commuter himself, has also been credited with making the system more user friendly with initiatives such as numbers passengers can call to find out when the next bus arrives at a stop.
But he also made the decision as Superstorm Sandy approached New Jersey to leave much of its rolling stock in low-lying yards, where engines and rail cars ended up underwater. NJ Transit has since opened yards at higher elevations.
Earlier this month, NJ Transit also had to cope with more than twice the number of expected football fans trying to get to the Super Bowl at Giants Stadium by rail. Weinstein pointed out afterwards that, while the rail link between Secaucus Junction and the stadium may have been a bottleneck, 40 percent of those who attended the game arrived by mass transit.
Ronnie Hakim, currently executive director of the New Jersey Turnpike Authority, is expected to replace Weinstein, the Star-Ledger said.