Chief Steve Abraira said in a letter that his resignation is effective Friday.
Thirteen deputies complained to Mayor Tom Menino in a letter in April that Abraira's failure to take command of the bombing scene was indefensible and part of a pattern of shirking leadership.
"You can unequivocally consider this letter a vote of no confidence in Chief Abraira," said the letter, which was first reported by The Boston Globe.
Abraira has said his command staff had the bombing scene under control and he acted according to national standards, which dictate the chief takes charge only if something's going wrong.
In his resignation letter, he wrote, "The baseless attacks by the Deputy Chiefs, especially their actions of making this a matter of public debate by leaking their letter of April 26th to the press, has made it impossible for me to continue to do my job."
He said he never had support from "a number" of department members because he was hired from outside the department in 2011.
Abraira, the city's first Hispanic chief, was also the first hired from outside the department's own union. He previously led the Dallas department and was an assistant chief in Miami.
Abraira thanked Menino and Fire Commissioner Roderick Fraser for their backing. Fraser had expressed confidence in his entire command staff, including Abraira. And a Menino spokeswoman had said the mayor had "full confidence in Commissioner Fraser to do what's best for the department," including his personnel decisions.
Copyright 2013 The Associated Press.