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Boughton's surgery was performed at the University of Pittsburgh Medical Center.
"The mayor is out of his surgery and recovering well," city spokeswoman Taylor O'Brien said. "His medical team is very pleased with the results of the surgery and are confident in his full recovery."
O'Brien also passed along a message from Boughton, 53, who is serving his eighth term as mayor of Danbury.
"He would like to extend his thanks for all of the encouragement, prayers and well wishes that he has received over the last 48 hours," she said.
Before heading into surgery early Tuesday, Boughton sent out a Tweet @MayorMark: "It's time. Thank all of you for your good wishes and prayers. God has the wheel now. "Clear eyes, full heart." #Danbury #1luv #fb"
The tumor, which was about the size of a lemon and located behind his left ear, is known as an Intracranial epidermoid cyst.
The popular mayor was diagnosed recently after suffering from dizzy spells and severe headaches.
City Council President Joseph Cavo is taking over work duties for Boughton, who could return for limited duties in as little as two weeks.
Boughton is up for re-election this fall for what would be his ninth term and is a Republican candidate for governor in 2018.
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