The president canceled a scheduled appearance in Northern Virginia to be present at the air force base for the arrival of the troops' remains, which was closed to media.
Thirty U.S. troops, including 22 Navy SEALs, and eight Afghan soldiers were killed Saturday when their Chinook helicopter was shot down by Taliban insurgents in the remote Tangi Valley near Kabul, the country's capital.
The downing of the helicopter was the largest single loss of military lives in the nearly decade-old war.
Obama's motorcade left the White House just after 11:30 a.m. EDT and arrived at Fort McNair about 15 minutes later, where four helicopters awaited him, his staff and reporters. The helicopters landed at Dover Air Force Base about 12:30 p.m. EDT.
The remains were returned to Dover in "unidentified" status until they are positively identified by the Armed Forces Mortuary Affairs Office.
Obama canceled a previously scheduled trip to Interstate Moving Services in Springfield, Va., where he planned to discuss new fuel efficiency standards for work trucks, buses and other heavy-duty vehicles. Instead, Obama met with industry officials at the White House to discuss the first-of-their-kind standards, the White House said.
The military has not identified the victims publicly. In cases where families have been informed, some have talked to the media.
In Afghanistan, military leaders vowed the overall war effort won't be compromised by the deadly incident.
U.S. Marine Gen. John R. Allen, who assumed command in Afghanistan just weeks ago, honored the slain troops. In a statement issued Tuesday, he said coalition forces would "continue to relentlessly pressure the enemy … and bring lasting and enduring peace to this historic land."
"Today, we honor the lives and service of our brave Americans and their valiant Afghan brothers in arms, who fought courageously against the enemies of the freedom and security of both our nations," Allen said in the statement. "In life they were comrades in arms, and in death they are bound forever in this vital cause. We cherish this selfless sacrifice."
Allen presided over the solemn ceremony at Bagram airfield near Kabul as the remains were loaded onto two C-17 cargo planes.
Western military officials confirmed Monday the helicopter had gone down as it was arriving to assist other troops engaged in fierce fighting, the Los Angeles Times reported. Military officials said no casualties were reported among the original ground force in the area, identified as U.S. Army Rangers.