Spokesman Josh Earnest said the United States welcomed the move, but pressed Pyongyang to free the two remaining Americans.
"While this is a positive decision ... we remain focused on the continued detention of Kenneth Bae and Matthew Miller and again call on the DPRK to immediately release them," Earnest said, referring to the country's official name of Democratic People's Republic of Korea.
The United States will continue to work actively on those cases, he added.
Fowle, 56, a street repair worker from Miamisburg, Ohio, was arrested in May for leaving a Bible at a sailor's club in the North Korean city of Chongjin, where he was traveling as a tourist. The communist state is particularly sensitive to religious proselytizing.
Miller was arrested in April for a separate incident. The longest to be held by North Korea is Bae, a Korean-American missionary arrested in November 2012 and sentenced to 15 years hard labor.
North Korea made it a condition of Fowle's release that the U.S. government transport him out of the country and set a time for him to be picked up, U.S. officials said.
"In this time frame the Department of Defenсe was able to offer a plane," State Department spokeswoman Marie Harf told reporters when asked if a military aircraft was used.
Passengers on another flight at Pyongyang airport reported seeing a blue and white U.S. military passenger jet, a stars-and-stripes emblem on its tail, parked on the tarmac on Tuesday afternoon, a source in Pyongyang told Reuters.
It was not immediately clear why reclusive North Korea decided to free Fowle. Washington has long insisted that the release of the prisoners should be unconditional and not linked to talks on North Korea's disputed nuclear programme.
Victor Cha, a senior adviser at the Center for Strategic and International Studies in Washington, said the release was a surprise and might signal a warming diplomatic trend.
"It is a surprising decision by the North Koreans, given their very inflexible stance over the past several months," Cha said.
"In North Korean eyes, Jeffrey Fowle's offenses may have been seen as the least severe (of the three U.S. prisoners) and therefore excusable."
HEADING HOME
After departing Pyongyang, the U.S. plane carrying Fowle flew to the Pacific island of Guam, site of a major U.S. Navy base, before leaving for the United States, Harf said.
U.S. officials declined to give details of the negotiations that led to Fowle's release, or to speculate why Pyongyang released him in case it jeopardized talks over Bae and Miller.
"We will let the North Koreans speak for themselves about why they decided to do this, and why now," Harf said. "While we are pleased he was able to leave, we urge the immediate release of the other two."
Harf said the release was facilitated by Swedish diplomats. Sweden has an embassy in Pyongyang and acts as a "protecting power" for Washington.
Stephen Haggard, a North Korea expert at the University of California in San Diego, said the move was likely part of an effort by Pyongyang to show it is "reasonable."
"North Korea is currently engaged in a very complex charm offensive on many fronts," said Haggard, citing Pyongyang's separate discussions with Japan on the fate of Japanese citizens abducted decades ago and secret talks with South Korea on recent border altercations.
