Frank DePaola, general manager of the Massachusetts Bay Transportation Authority, will step down on June 30 because of health concerns, a little over a year since he took the reins of the embattled agency.

In a written statement, DePaola disclosed he has cancer and wants to focus on his treatment.

“My decision to retire is a difficult one, but I cannot continue to spend the countless hours the job demands while continuing needed treatment and focusing on my health,’’ said DePaola, who was recently absent for more than two weeks for medical reasons.

The MBTA’s chief administrator, Brian Shortsleeve, will take over as acting general manager in July. Chief Operating Officer Jeffrey Gonneville will also take on additional responsibilities, such as overseeing the T’s safety and accessibility departments, according to officials.

The change in leadership will be another big challenge for the agency, which officials have pledged to improve since its disastrous performance during the record-breaking storms of the winter of 2015.

Joseph Aiello, head of the fiscal control board created to oversee the T, said DePaola’s departure would be a “devastating blow’’ to the organization.

“It’s always difficult to have a change in leadership, but I would say in particular, it’s challenging when you’ve had such an effective person,’’ he said.

In a memo to colleagues, Transportation Secretary Stephanie Pollack said she will consult with T leaders and the state’s two transportation boards to establish a long-term plan for the leadership at the agency. Aiello gave no timeline for the appointment of a permanent leader to replace DePaola but said the agency must “get organized’’ before embarking on an effective search.

“We’ve made some appointments to get us through an interim period, but we still need to figure out the solution to this for a permanent general manager,’’ he said.

DePaola, who served as the highway administrator and chief operating officer of the state transportation department, was appointed to the post of general manager in March 2015, shortly after Beverly Scott abruptly announced her resignation.

At the time, the agency was embroiled in controversy as the transit system struggled to operate that winter. Within months, the agency would face another crisis, as the agency revealed that its long-awaited Green Line extension project could be $1 billion over budget.

DePaola oversaw the organization during a tumultuous period filled with change. In 2015, a law pushed by Governor Charlie Baker created a fiscal and management control board that was to remain focused on improving the finances and service for the long-maligned agency.

The agency also appointed Shortsleeve to a newly created chief administrator post, which was meant to focus on finances while the general manager job remained attuned to the operations of the agency.

By the end of the year, the fiscal and management control board announced that DePaola would stay at his post until at least June 30.

DePaola, a Brockton native, is well-respected and well-liked at the MBTA, where he previously worked as an assistant general manager for the design and construction department. He also worked as director of construction at the Massachusetts Water Resources Authority.

Jim Aloisi, a former transportation secretary who closely watches the politics of the agency, called DePaola a “first-rate public servant.’’

“He’s one of those people who are very talented, who doesn’t have an ego, and that’s pretty rare,’’ said Aloisi.

Governor Charlie Baker praised DePaola in a prepared statement.

“Frank has been the kind of general manager that the MBTA needs, someone whose management style has helped the MBTA to increase the public’s confidence in the transit system’s performance while also leading the T workforce during a period of change,’’ he said.

In a note to colleagues, Pollack also lauded DePaola for his willingness to serve.

“When I walked into Frank’s office to ask if he’d step in as interim GM, he showed me the work he had already begun, not just on recovering service but on planning for a springtime push to get a head start on repairs that would be needed before the next winter,’’ she wrote. “I knew I had the right guy.’’

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