MBTA General Manager Beverly Scott announced Wednesday that she will resign this April after an embattled couple of weeks for the transportation agency.

In a resignation letter, Scott said she would ensure a “smooth transition’’ and work with the MassDOT Board of Directors to help find her replacement over the next 60 days. Her final day in office will be April 11.

“It goes without saying that the MassDOT Board and the new Administration can count on me to stay fully engaged throughout this period,’’ she wrote.

Scott first took the job in December 2012 and previously held senior positions with other metropolitan transit authorities, including the MTA in New York. According to a bio published on the MBTA website, Scott has worked in public transit for nearly 30 years.


Scott told reporters during a press conference Tuesday that she would not comment on whether or not she should resign.

“I’ve always…told people, if you ever think that there is anybody else that you think could do it better, they should do it,’’ she said.

“The Governor and Lt. Governor were surprised to learn of Dr. Scott’s resignation this afternoon,’’ a statement from Governor Charlie Baker’s office read. “They thank her for her contribution to the Commonwealth and are grateful for her offer of assistance as the MBTA transitions to a new General Manager. The Governor looks forward to meeting with MBTA officials tomorrow, working with them to assess the issues that have plagued the agency in recent weeks and developing operational and maintenance plans moving forward.’’

“I thank Dr. Beverly Scott for her deep commitment to our public transportation system and to the people of Boston and the Commonwealth,’’ Boston Mayor Marty Walsh wrote in a brief statement. “She has shown leadership and courage during the challenges we are facing, and I wish her the best of luck in the future.’’

The MassDOT Board’s chairman John Jenkins wrote that he was also “stunned’’ by the news in a statement. The board unanimously approved a vote of confidence in favor of Scott only hours before her decision was made public.


“This board has had no discussions at any time about her tenure as General Manager,’’ he wrote. “We hoped and expected that she would fulfill her three year contract, which ends in December of this year. I want to thank Dr. Scott for her skillful and committed leadership over the last 26 months, and wish her the very best as she moves on to her next challenge.’’

Jenkins said he would appoint a subcommittee “in the coming weeks’’ to direct a search for the agency’s new chief executive.