"Abbas Zaidi has resigned and we have accepted his resignation," newly appointed PCB chief Nasim Ashraf told reporters after a meeting of the board in the eastern city of Lahore.
Zaidi's departure comes three days after former PCB chief Shaharyar Khan quit and two days after spinner Mushtaq Ahmed was sacked as assistant coach for the Champions Trophy.
Pakistan cricket has been in the spotlight since August's Oval Test against England when captain Inzamam-ul Haq refused to take his team back on the field after it was accused of ball-tampering.
Inzamam was acquitted of tampering but was handed a four-match ban for bringing the game into disrepute. His replacement Younis Khan last week refused to lead the side, saying he did not want to be a "dummy" captain.
The refusal prompted Khan to resign. His successor Ashraf reinstated Younis on Saturday, hours before the team's departure for India and the Champions Trophy.
Ashraf said that Inzamam would captain Pakistan against the West Indies, who are set to tour here in November and December for three Tests and five one-day internationals.
"Inzamam will lead Pakistan in the home series against the West Indies because Younis was only appointed for the Champions Trophy," he said.