The change at the top in the Foreign Office also saw a minor reshuffle of senior officials, including Foreign Office Spokesman Masood Khan, who has been posted as the Permanent Envoy to the United Nations, media reports said.
Riaz Khan, who was the Foreign Ministry Spokesman before being posted as Pakistan's envoy to China, would formally take over as the Foreign Secretary tomorrow.
Khokhar made a farewell call on President Pervez Musharraf who appreciated his services to Pakistan.
Significantly, the change of guard in Pakistan's Foreign office is taking place on the eve of External Affairs Minister K Natwar Singh's visit to Islamabad.
This is the first bilateral visit by Indian External Affairs Minister in about 17 years. Singh visited Pakistan last year to take part in SAARC Foreign Ministers meeting.