Although the CIA's announcement comes less than a day after agency chief George Tenet unexpectedly resigned, the intelligency agency insists no link exists between the two.
"Pavitt made the decision to retire about a month ago, and his departure is unrelated to director of central intelligence George J. Tenet's resignation announcement yesterday," a CIA statement said on Friday.
Pavitt, 58, has worked for the CIA since 1973 and held various positions in Europe and Asia before his rise to deputy director of operations since 1999.
As spymaster and the man responsible for covert operations conducted by the CIA, his identity remained a secret until recently.
Pavitt's deputy Stephen Kappes is expected to take over as deputy director of operations.