Chief Steve Abraira said in a letter that his resignation is effective Friday.
Thirteen of the department's 14 deputy chiefs complained to Mayor Tom Menino in letter 11 days after the April 15 bombings that Abraira's failure to take command of the 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."
Fire commissioner Roderick Fraser accepted Abraira's resignation and wishes him well, said fire department spokesman Steve McDonald.
The department's current chief of operations, John Hasson, has been named acting chief, McDonald said. Hasson was one of the 13 deputy chiefs who signed the April letter.
A woman who answered the phone Monday at the Boston Firefighters Local 718 said union officials weren't commenting on Abraira's resignation. Menino's office referred comment to McDonald.
Abraira, the city's first Hispanic chief, was also the first hired from outside the department's own union. He led the Dallas department and was an assistant chief in Miami before coming to Boston in 2011.
In his resignation letter, Abraira said his outsider status hindered his efforts to fulfill his mission to modernize the department.
"A number of members ... preferred that the Chief be selected from within the ranks of the Department itself," he wrote.
"I think it is also fair to say that unfortunately a vocal and aggressive minority of the members of the Department did not support our efforts," he said.
Abraira thanked Menino and Fraser for backing him during "countless occasions" when they "resisted both private and public efforts to undermine my authority and to compromise my ability to carry out the mission."