"Abbas Zaidi has resigned and we have accepted his resignation," newly appointed PCB chief Nasim Ashraf told reporters in 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.
The country's cricketers have been in the spotlight after they forfeited their final Test against England after they were accused of ball tampering.
Captain Inzamam ul-haq 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 be reinstated as captain of Pakistan against the West Indies, who are set to tour 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.