Haradinaj, who resigned a day earlier as prime minister of Kosovo, arrived at the airport accompanied by his wife and surrounded by well-wishers, before boarding a special flight to The Hague.
He is facing charges over his role in Kosovo's 1998-1999 war against Serbian aggression from the former Yugoslavia.
Officials said Haradinaj was indicted by the International Criminal Tribunal for the former Yugoslavia (ICTY), and would be presented to the court later on Wednesday.
Nato peacekeepers were out in force to prevent any outbreak of violence, with troops posted at each intersection on the road to the airport and a surveillance aircraft overhead.
Haradinaj, an ethnic Albanian, was a rebel commander during the uprising against Serbian rule and remains a hero to many Kosovo Albanians, who revere him as a freedom fighter.
Kosovo Serbs and the government in Belgrade, however, see him as a terrorist responsible for atrocities against Serb civilians during the conflict, which ended after a Nato bombing campaign forced Serbian forces to withdraw.
"I want to tell you that I am innocent of all the crimes of which I am accused," Haradinaj, 35, said on Tuesday as he announced his resignation, adding that his indictment was the result of Serbian lies against him.
"I want to tell you that I am innocent of all the crimes of which I am accused"
ex-Kosovo Prime Minister
Haradinaj's decision to step down and surrender was praised by the international community, which also called for calm among his supporters in the mainly ethnic Albanian province which is seeking independence from Serbia.
US State Department spokesman Richard Boucher said Washington welcomed Haradinaj's resignation but warned that violence from his supporters would damage their hopes for independence.
"His actions demonstrate his deep concern for the future of Kosovo and its people," Boucher said.
The province's progress towards meeting UN-set democratic standards is set to be reviewed later this year before a decision is made on whether to start talks on the ethnic Albanians' independence demands.
"In order to receive a positive assessment from the comprehensive review later this year and to begin a process to determine its future status, Kosovo must preserve peace and continue to work to implement the standards," Boucher said.
German Foreign Minister Joschka Fischer stressed the importance of compliance with the UN war crimes tribunal for the all the former Yugoslav republics.
"I assume that it was a well thought-out step and thus I hope that all those involved understand how important cooperation (with the tribunal) is," he said.
Britain called on "all people in Kosovo not to exploit the fact of the indictment for their own ends", Denis MacShane, junior Foreign Office minister responsible for Europe, said.
"Violence is unacceptable and will retard Kosovo's prospects."
Nato troops currently protect
Kosovo's ethnic Serb minority
In Belgrade, Serbian newspapers on Wednesday focused on security concerns for the Serb minority in Kosovo, which lives in isolated enclaves protected by Nato troops.
Nato was criticised by human-rights groups and the Serbian government for failing to stop ethnic Albanian mobs which rampaged through Serb enclaves for three days a year ago, leaving 19 dead and thousands homeless.
Nato sent an extra 1000 British and German troops to the province, boosting its overall Kosovo mission strength to some 19,000 soldiers in the days leading up to Haradinaj's resignation.