"With decisive and strategic decision-making, we succeeded in earning the goodwill and respect of the global cricketing family, which I am hopeful will lead to increased international cricket being hosted in Pakistan in future."
Khan added it was "hugely satisfying" to see the resumption of Test cricket, which has included recent tours by South Africa, Sri Lanka, Bangladesh and Zimbabwe.
But Pakistan is again facing cricketing isolation after New Zealand called off their first tour of the country in 18 years earlier this month over security concerns.
Their decision was swiftly followed by England's cancellation of a planned tour in October.
"(The) Pakistan Cricket Board today confirmed Wasim Khan has tendered his resignation as chief executive," the PCB said in the statement.
The PCB's board of governors later met by videoconference during which they unanimously accepted the resignation.
Khan, who is British with Pakistani heritage, was hired on a three-year contract in 2019 and had organised Pakistan's tours of England and then New Zealand amid severe Covid-19 restrictions last year.
The first British Muslim to play county cricket in England, he had reported run-ins with former PCB chairman Ehsan Mani, who he accused of stopping him from working freely.
Pakistan was forced to play its home matches at neutral venues in the United Arab Emirates after the terrorist attacks on the Sri Lankan team bus in 2009.
Security in the country has improved dramatically over the past few years, but militant groups still operate along the border with Afghanistan.
Pakistan has only hosted South Africa, Sri Lanka, Bangladesh and Zimbabwe since the 2009 attacks.