Joe Lhota has resigned as chairman of the Metropolitan Transportation Authority, the latest in a series of departures from the administration of New York Gov. Andrew Cuomo as he prepares for a third term.

Fernando Ferrer, the MTA’s current vice chairman, will take the reins as acting chairman of the authority’s board and will run its meeting on Thursday, according to a state official.

Mr. Lhota, 64 years old, was appointed chairman of the authority last year amid rising delays on the New York City Subway. But he accepted the assignment on a part-time basis, retaining his job as chief of staff at NYU Langone Health, and delegated responsibility for much of the day-to-day operations of the authority to President Patrick Foye and managing director Veronique Hakim.

In a statement, Mr. Lhota said he took the position for the “sole purpose of halting the decline of service and stabilizing the system for my fellow New Yorkers.” He touted an $800 million emergency repair package that he crafted in his first month, as well as a new executive team he put in place.

In September, the number of total train delays fell to the lowest point since February 2016, Mr. Lhota said. “There is still a long way to go to achieve the performance that New Yorkers demand and deserve,” he said.