The Islamabad station chief, one of the agency's most-important positions in the world, arrived only late last year after his predecessor was essentially run out of town when a Pakistani official admitted his name had been leaked, ABC News reported.
The top CIA officer in Islamabad, who was supervising the team that tracked down bin Laden, left Pakistan due to medical reasons and is not returning, it said.
The departure of two station chiefs in such a short span of time threatens to upset a vital intelligence office, it said.
US officials, however, insisted that the quick turnover would not harm US intelligence efforts in Pakistan, it said.
That is because, according to three US and Pakistani officials, the departing chief of station had an "extremely tense" relationship with his ISI counterparts, including Director General Lt Gen Ahmad Shuja Pasha. One US official said the CIA chief was dying to depart in a few months as a result of his poor relations with the Pakistanis, it said.