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Dr. Gottlieb, whose wife and three children have remained in their Westport, Conn., home since he took office, said he was weary of the commute and missed his family.

Dr. Gottlieb had been subject to increasing pressure from some Republicans in Congress and his former associates in the conservative movement, for his tough stance against youth vaping and traditional cigarettes. A coalition of influential conservative groups recently asked the White House to block some of the key parts of the F.D.A.’s strategy to prevent youths from vaping; and Republican Senator Richard Burr blasted the commissioner on the Senate floor for his proposal to ban menthol cigarettes.

Dr. Gottlieb said these protests had no role in his departure.

“There’s no intrigue here,” he said, adding that he planned to advance the agency’s pending tobacco regulations before he leaves, in about one month.