Michael P. DePallo, a former transit leader from New York, stepped down two years after he replaced John Fenton, who left the top post unexpectedly in 2012 to head a Florida-based freight railroad.
DePallo, who could not be reached for comment, announced at the end of a Metrolink board meeting that he would depart Jan. 2 to pursue other opportunities.
"Metrolink has a talented staff and a dedicated forward-looking board that are committed to safety and innovation and will continue to do great things to enhance mobility for the Southern California region," DePallo said in a prepared statement.
Metrolink, which has about 42,000 weekday boardings and 512 miles of track, serves Los Angeles, Orange, Riverside, San Bernardino, San Diego and Ventura counties.
DePallo's resignation comes less than a month after the railroad's chief auditor, Barbara Manning, was placed on leave. Jeff Lustgarten, a railroad spokesman, said the board terminated her Friday. Three chief financial officers have also left the railroad in the last year.
Metrolink officials declined to discuss DePallo's departure because personnel matters are confidential.
Bart Reed, executive director of the nonprofit Transit Coalition, said he was not surprised by the resignation. "Metrolink is a challenging place," he said. "The problem with the railroad is that there are too many masters on the board with conflicting demands that are difficult to meet."
DePallo joined Metrolink in September 2012 at a difficult time in the railroad's efforts to build ridership, upgrade operations and improve safety in the aftermath of the deadly Chatsworth crash in 2008. In that collision, 25 people died and 135 were injured when a Metrolink engineer missed a stop signal while text messaging on a cellphone and struck a freight train head on.
Among the key initiatives since then were programs to deploy safer rail cars and a $200-million positive train control system, a sophisticated electronic network to monitor trains and take control of them if necessary to avoid accidents.
But problems surfaced at Metrolink early last year, when a scathing report revealed accounting irregularities, poor management and flaws in record keeping. The report described the financial management system as a "morass."
More recently, DePallo has had to deal with a rash of failing ticket vending machines, declining ridership and increasing breakdowns in the railroad's aging fleet of locomotives. On Friday, a report presented to the board suggested changes in the railroad's governing structure, including turning the operation over to a local transit agency.
"We've had our share of challenges in the past few years," Lustgarten said. "Today, we are in a much more stable and healthy financial position than we were six months ago. We have a new chief financial officer and a new finance team that have done an incredible amount of work. New controls are in place and they have initiated a new financial management system."
Railroad officials credit DePallo with furthering the positive train control project, pursuing the purchase of cleaner-running locomotives and addressing the financial issues.
"Metrolink has a great history and a bright future," board Chairman Larry McCallon said in a prepared statement. "We are especially proud of this organization's commitment to public safety as we remain on track to be the first commuter railroad in the country to implement positive train control."