The trip, shrouded in secrecy until his arrival amid security concerns, opened with talks with President Hamid Karzai at his Kabul palace, which Obama used to press for a stepped-up fight against corruption and the drugs trade.
"The American people are encouraged by the progress that has been made," Obama told Karzai after the one-on-one meeting, which included an invitation for the Afghan leader to visit Washington on May 12.
But Obama also pressed Karzai, with whom he has had a testy relationship, to "continue to make progress" on the civilian front, including on good governance, the fight against corruption and the rule of law.
He also said he had made the dramatic through-the-night flight to Afghanistan to thank US troops for their "incredible efforts" and their "tremendous sacrifices" a long way from home.
Karzai thanked American taxpayers for helping "the rebuilding and reestablishing" of Afghanistan civilian institutions and government.
Obama landed in Afghanistan amid a spike in deaths of foreign troops in the escalating war, and as the first big offensive of his new strategy unfolds in Helmand province, with Taliban strongholds in Kandahar among future targets.
After touching down after dusk, Obama flew by helicopter to the palace with key aides, including Rahm Emanuel, his chief of staff and political advisor David Axelrod, said an AFP photographer traveling with the president's party.
The visit, expected to last only a few hours in the unstable Afghan capital, was also scheduled to include in-person briefings for Obama by war commander General Stanley McChrystal and US ambassador to Kabul Karl Eikenberry.
Obama and Karzai met almost immediately after he touched down, and emerged from the palace on a red carpet for a welcoming ceremony, including an Afghan guard of honor and the US and Afghan national anthems.
Private, and likely candid talks between the two leaders were followed by an expanded session with the Afghan cabinet and a shared meal.
Obama landed in Afghanistan emboldened by the best week of his presidency, after passing a historic health care reform law and concluding a major nuclear arms control treaty with Russia.
But the Afghan war, and his fateful decision to surge more troops into a conflict launched after the September 11 attacks in 2001, still holds the capacity to humble his presidency.
Obama announced in December that he was pouring 30,000 more troops into Afghanistan, in a gamble he said was designed to "seize the initiative" to end the unpopular war and start a US pullout in July 2011.
Since then, US public opinion has stabilized slightly, despite increasing fighting, with a CNN/Opinion Research poll last week finding opposition to the war had dropped below the 50-percent mark for the first time in nearly a year.
Fifty-five percent of Americans now approve of how Obama is handling Afghanistan, up from 42 percent late last year when the president agonized for months over his strategy, before announcing the surge in December.
The United States and NATO have more than 121,000 troops in Afghanistan, set to rise to 150,000 by August as part of the new plan to reverse the Taliban momentum, particularly in the south, and hasten an end to the war.
Obama's last visit to Afghanistan came when he was a senator and Democratic presidential nominee in 2008 -- but since then he has been involved in a long-distance battle of wills with Karzai, who won re-election last year.
US national security advisor James Jones said on Air Force One that Obama would try to make Karzai understand "that in his second term, there are certain things that have been not paid attention to, almost since Day One.
"That is things like... a merit-based system for appointment of key government officials, battling corruption, taking the fight to the narco-traffickers, which fuels, provides a lot of the economic engine for the insurgents."
The fast-track war strategy envisages that American troops would start coming home in July 2011, though a full withdrawal could take several years.
Most of the 10,000 extra troops that have arrived so far have been sent to the volatile south, the spiritual heartland of the Taliban insurgency.
More than 105 foreign troops have been killed this year, more than double the number who died in the first two months of 2009.
Source: AFP South Asian Edition