"I've had a good career," he said. "I'm ready to enjoy my grandchildren."
The agency will soon begin another search for someone to oversee the system of buses, trains and trolleys that transports about 750,000 people a day.
The SEPTA board will first look inside to replace him, SEPTA board member Michael O'Donoghue said. Top candidates are treasurer Fay Moore and assistant general manager Pat Nowakowski, he added.
"We should not necessarily immediately kick off a national search," O'Donoghue said. "Let's look inward and see if we have somebody on our own current staff who could fill this job."
When he began his tenure at SEPTA in 1996, Leary inherited a mostly alienated board of directors and a steadily decreasing ridership. Many board members had been deeply mistrustful of former general manager Louis J. Gambaccini and wary of deficit spending.
In this atmosphere, Leary performed admirably, said Rick Wooten, a SEPTA board member and former longtime agency official.
"He stabilized SEPTA. We're not in a crisis mode on the financial side, operationally, or on the capital side," said Wooten, who is also a transit lobbyist in Harrisburg. "It's not glamorous. But it is fundamentally and basically the most important thing.
"Why would anyone want to stay there more than five years?" he added.
Backed by a board focused on the bottom line, and in a political environment hostile to transit funding, Leary forced streamlining at SEPTA.
The agency had balanced budgets in four of his five years, he pointed out.
The savings, however, came at a cost.
While Leary extracted flexible work rules from the Transport Workers Union Local 234, SEPTA's largest labor unit, the 1998 contract dispute sparked a 41-day strike, the second-longest in SEPTA's history.
The concessions saved SEPTA $18 million over the life of the contract to invest in new service, but left labor officials bitter.