Friday's action followed a special closed-door meeting of Metra's board, one of several it has held in recent months.



Clifford attended the beginning of the Metra board but left after the agreement was discussed during the closed session. He apparently walked out of Metra headquarters immediately and was not available for comment.



Clifford's three-year contract was set to expire in February 2014. He needed the support of a "supermajority," or eight of the board's 11 members, to have his contract renewed.



Clifford, a native of the Los Angeles area, had been hired to put the commuter rail agency back on track following the 2010 suicide of Pagano, its disgraced executive director.



Pagano, 60, stepped in front of a Metra train near his Crystal Lake home on May 7, 2010, after an investigation revealed he had taken $475,000 in unapproved vacation pay and forged memos to cover it up.



Clifford took over in February 2011 under a three-year contract that paid him $252,500 annually. A Marine Corps veteran, he came from LA's Metropolitan Transportation Authority, or Metro, where he served as general manager of one of the bus service sectors.



The change at the top will affect Metra's 300,000 daily riders, who have seen hefty fare increases in the last two years. Under Clifford, there have been reforms and customer friendly upgrades as the agency finally rolled into the 21st century, transportation experts say.



Earlier this year, Clifford presented the board with a long list of accomplishments, taking credit for financial savings, administrative achievements and customer service enhancements. The agency also has ended the practice of diverting money intended for equipment and infrastructure to day-to-day-operations, Clifford pointed out.



Metra has exceeded its 95 percent on-time performance goal, even after ending a practice that inflated the numbers, Clifford said.