The man was identified only by his surname, Kim, according to the BBC.
He becomes the third American to be detained by the North; one has been sentenced for spying, the other for trying to steal a sign from a hotel.
The latest detention comes amid high tension on the peninsula, with the US warning its “strategic patience” on the North’s nuclear programme is over.
A US naval battle group headed by an aircraft carrier, the USS Carl Vinson, and described by President Donald Trump as an “armada”, is expected to reach the Korean peninsula later in the week.
The South Korean news agency Yonhap said the detained American citizen, in his 50s, was a former professor from Yanbian University in China and had been in North Korea for a month in connection with relief programmes.
He was arrested at Pyongyang International Airport, Yonhap said.
In January last year, US student Otto Warmbier, 21, was arrested for trying to steal a propaganda sign from a hotel while visiting North Korea.
He was given 15 years’ hard labour for crimes against the state in March 2016.
In April last year, Kim Dong-chul, a 62-year-old naturalised US citizen born in South Korea, was sentenced to 10 years’ hard labour for spying. He had been arrested the previous October.
The US has in the past accused North Korea of detaining its citizens to use them as pawns.
After the brother of North Korean leader Kim Jong-un was murdered recently in Malaysia, Malaysian citizens in Pyongyang were arrested and held until North Koreans suspected of the murder were released in Kuala Lumpur.
Tension remains high on the peninsula following the North’s recent failed missile test and massive military parade showing off its latest hardware.
North Korea has said it is ready to sink the Carl Vinson, and on Sunday said it would strike Australia with nuclear weapons if it remained an ally of the United States.
North Korea’s aim is to develop nuclear weapons small enough to put on ballistic missiles, but there is no evidence yet it has done so, or that it has missiles with the range to reach long-distance targets.
This week US Secretary of State Rex Tillerson, on a tour of Asian nations, said the US was “reviewing all the status of North Korea, both in terms of state sponsorship of terrorism as well as the other ways in which we can bring pressure on the regime in Pyongyang”.
North Korean media responded by warning of an unspecified “super-mighty pre-emptive strike”.
Timeline of recent tensions
- 8 April: The US military orders a navy strike group to move towards the Korean peninsula
- 11 April: North Korea says it will defend itself “by powerful force of arms”
- 15 April: North Korea puts on a huge military parade – complete with missiles – to mark 105th birthday of the nation’s founding president, Kim Il-sung. Meanwhile US Vice-President Mike Pence arrives in South Korea
- 16 April: North Korea conducts a rocket test, but it fails
- 17 April: Senior North Korean official tells the BBC the country will continue to test missiles “weekly” and Mr Pence warns North Korea not to “test” Donald Trump
- 18 April: It emerges the US Navy strike group was not heading towards North Korea when US officials suggested it was.