One day after the Massachusetts Bay Transportation Authority became the subject of controversy resulting from the decision to halt nearly all services Tuesday due to snow, MBTA General Manager and CEO Beverly Scott announced her resignation in a Wednesday letter addressed to the Massachusetts Department of Transportation board chairman John Jenkins.

Scott, who is set to vacate her position on April 11, thanked the MassDOT board of directors in her letter of resignation, and said that she will work with them over the next 60 days to facilitate a smooth transition.

“No question, much more remains to be done to achieve the modern, and first class public transportation system that all want and deserve,” Scott said in the letter. “At the same time, on a personal professional note, the opportunity to be a part of the [former Massachusetts Gov. Deval] Patrick administration transportation team and share in a small part of the transportation gains over the past several years has been more than worth the effort.”

Jenkins responded to Scott’s resignation with surprise in a statement issued Wednesday.

“I am stunned by the resignation of Dr. Scott. Be clear, this Board has had no discussions at any time about her tenure as General Manager,” he said in the statement. “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. In the coming weeks, I will appoint a sub-committee of the Board to direct a nationwide search for her replacement.”

When asked about the circumstances leading up to the resignation and the MBTA’s next steps, Michael Verseckes, a spokesperson for MassDOT, said there were no plans for what actions the department would take to compensate for the loss.

“The letter and the statement from the chairman, that’s really all we have,” he said. “In the statement, the chairman said he was going to assemble a committee to begin.”

Scott’s resignation follows criticism directed at Massachusetts transit system for the poor condition of the transportation systems in the wake of Boston’s historic snowfall over the past three weeks. Tuesday’s decision to shut down the MBTA altogether caused many to doubt the fitness of the aging system.

Massachusetts Gov. Charlie Baker met with MBTA officials Thursday to discuss the recent problems with the transit system, said Tim Buckley, a spokesman for Baker, in a Wednesday statement.

“The Governor and Lt. Governor were surprised to learn of Dr. Scott’s resignation this afternoon. They thank her for her contribution to the Commonwealth and are grateful for her offer of assistance as the MTBA transitions to a new General Manager,” Buckley said in the statement. “The Governor looks forward to meeting with MTBA 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.”

Boston Mayor Martin Walsh said in a Wednesday statement he will also be working with Baker in the coming weeks and said he remained focused on helping advance Boston’s public transportation system.

“I thank Dr. Beverly Scott for her deep commitment to our public transportation system and to the people of Boston and the Commonwealth,” Walsh said in the statement. “She has shown leadership and courage during the challenges we are facing, and I wish her the best of luck in the future. I look forward to working with the Governor to improve our public transportation system to better serve our residents who rely on it every day.”

Several residents said that while the T’s inconsistent service is inconvenient, there is nothing anyone, including MBTA officials, can do about the unprecedented amount of snow.

Andres Hernandez, 26, of Fenway, said he was on his way to a conference when he found out the T was down and had to walk from downtown to Fenway to make it on time.

“I left early, went to the T, and it wasn’t working, so I had to walk all the way from down town just to get here,” he said.

Brenda Velez, 49, of Fenway, said the real problem lies in the state of the trains, not the weather or leadership.

“The train system in Boston is a nightmare regardless of the season,” she said. “It needs money and new trains.”

Ben Virkus, 23, of Allston, said Scott’s resignation was unnecessary, and closing down the city is not ideal, but sometimes warranted.

“It is ridiculous that the director has to step down,” he said. “It’s a big decision to step down, but I don’t think it was necessary. This was a freak weather incident. There is no city that wants to close.”