The move comes just eight months after the company took over the operation of a system that provides 129,000 rides every weekday to passengers in the Boston area.

Thomas M. Mulligan has been replaced by his deputy, Gerald Francis, as head of Keolis Commuter Services, two people with direct knowledge of the decision said Wednesday.

Under fire for weeks of poor performance, the French company that runs the MBTA’s commuter rail system has replaced the general manager of its Boston operation — the second major management change this month atop the region’s snowbound public transportation network.

The change also follows nearly a month of public outrage after one of the snowiest winters on record crippled the commuter rail system and the MBTA’s subway system, prompting Governor Charlie Baker to declare that he was “done with excuses” from Keolis.


Francis takes over the top spot at Keolis with experience in controversy. He was deputy general manager for the Washington Metropolitan Area Transit Authority in Washington, D.C., in 2009 when a crash killed nine people.

According to minutes of a Senate committee hearing following the fatal accident, US Senator Barbara Mikulski blasted the agency’s leaders for “a pattern of laxity, passivity, and lip service.”

Francis was one of five senior executives who stepped down or were reassigned at the time, according to the Washington Post. A subsequent report by the National Transportation Safety Board on the fatal crash described a “lack of safety culture” at the authority.

Francis later served as the Herzog Transit Services general manager of California’s Caltrain system, after which he came to Boston.

On Wednesday, a Keolis spokesman did not respond to requests for comment on the change in leadership.

Mulligan’s departure is the second major administrative shake-up this month in the public transportation system. On Feb. 11, MBTA general manager Beverly A. Scott announced her resignation.


On Wednesday, officials announced that Frank DePaola will serve as MBTA interim general manager until Scott’s permanent replacement is chosen.

DePaola is the former acting transportation secretary, and has served as highway administrator and the chief operating officer of the state Transportation Department.

The MBTA oversees the Boston-area subway system, and contracts operation of the sprawling commuter rail system to Keolis.

Keolis, which also runs commuter rail lines in Northern Virginia, won an eight-year, $2.68 billion contract to take over the Boston area’s commuter rail service in July from the Massachusetts Bay Commuter Railroad Company, which had operated the system since 2003.

The French company established Keolis Commuter Services, and shortly after it took control of the MBTA commuter rail system it named Mulligan, who had previously worked for Union Pacific and Amtrak, general manager.

Even before a record-breaking onslaught of snow hit the state, the company had faced tough questions about its on-time performance rates.

At a meeting for the Department of Transportation’s board of directors, Mulligan blamed some of the unreliable service on the commuter rail’s decades-old equipment.

The snowiest winter in two decades further hobbled the service’s performance, prompting the rebuke from Baker. The governor has since become more involved with the operations of the MBTA and Keolis, sending senior staffers to work with the transit systems for much of last week.

On Friday, Baker announced a seven-person advisory panel charged with looking into the finances, governance and maintenance from the MBTA and its commuter rail system.


The group, made up of renowned transportation and infrastructure specialists, has been ordered to present the governor with recommendations to improve the system by the end of the March.

Tim Buckley, a Baker spokesman, said that the governor would be meeting again with Keolis officials on Thursday.

In recent days, the commuter rail has operated with fewer last-minute delays and cancellations.

But that has been only after the service switched to a limited schedule that reduces service by dozens of trains, and has riders still fuming.

Martha Cesarz, a Swampscott rider who uses the Newburyport/Rockport line daily, predicted dire consequences if the service is not fixed soon.

“It’s going to destroy the economy of Boston because people are going to get fed up,” she said.

Similar complaints have plagued the T, where DePaola, the new interim general manager, will start next Wednesday.

DePaola has a master’s degree in civil engineering from Northeastern University, and has worked as an MBTA assistant general manager for design and construction.

In a statement, DePaola said he was hoping to implement a strategy to restore the system to “full strength,” and restore customers’ faith in the service.

The chairman of the Transportation Department’s board of directors has said it plans to conduct a nationwide search for a permanent general manager.

The state’s transportation secretary, Stephanie Pollack, has said the board wanted an interim leader to ease the transition, and praised DePaola in a statement.


“With the depth and breadth of Frank’s experience as an engineer, a manager, and a problem-solver, I have full confidence that he has the skill sets and capabilities to serve as Interim General Manager,” she said.

Joe Pesaturo, a spokesman for the T, said Scott will stay on until April to assist with the transition.

The governor’s office also released a statement on the appointment, thanking Scott and DePaola for their work during the transition period.

“As the governor’s MBTA review panel continues its work, Mr. DePaola and Dr. Scott’s input will be invaluable to improving public transit services for the residents of the Commonwealth,” the statement said.

On Wednesday, the Transportation Department also announced Thomas Tinlin, the state’s chief of highway operations and maintenance who has served as Boston’s transportation chief, will serve as acting highway administrator.

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Nicole Dungca can be reached at nicole.dungca@globe.com. Follow her on Twitter @ndungca.