Khanfar, who has led the network for eight years, said that his goal had been to “establish Al Jazeera as a global media leader,” and that the “target had been met”.
The man widely seen as the face of Arab media will be replaced by Sheikh Ahmad bin Jasem al-Thani, a member of Qatar’s ruling family and a member of a top body at state-run Qatargas.
In a posting on Twitter, the Palestinian-born correspondent said: “Eight years is a long time to be leading a network. Renewal and change is always good.
“I think everyone will agree that Al Jazeera is stronger than ever. Our coverage has been exceptional and is now widely viewed.”
Since it was launched in 1996, Al Jazeera has become the highest-profile satellite news broadcaster in the Middle East. It has frequently had difficulties with Western and Arab governments in a region where governments have traditionally kept tight control over state media.
Al Jazeera, owned by the Qatari government, aired round-the-clock coverage of uprisings that brought down veteran rulers in Tunisia, Egypt and Libya this year, and the station promotes itself as a democratic voice in the region.
In a note to staff, Khanfar, a former correspondent in Iraq and Africa, said media independence had been a “contradiction in terms” before Al Jazeera’s launch.
“State media was prevalent and was blatantly used for propaganda and misinformation. Within such an environment the public probably doubted that Al Jazeera would fulfill its promise of independent journalism,” he said.
“We managed to pleasantly surprise them by exceeding all expectations.”
But critics say the network is more timid in covering events closer to its Gulf home, and the cameras of its main Arabic channel were notably absent during a month of similar protests in the Gulf Arab state of Bahrain which the government crushed in mid-March.
Al Jazeera’s bureau chief in Lebanon, Ghassan Bin Jiddo, resigned in April, apparently in disagreement over its coverage of the revolts, which have also engulfed Syria and Yemen.
Leaked US diplomatic cables described the channel as a tool in Qatari diplomacy. The channel has played an important role in raising the prestige of the small, wealthy Gulf Arab state.