The man, a Korean-American in his fifties identified only by his surname Kim, had been in North Korea for a month to discuss relief activities, Yonhap said on Sunday. He was arrested at Pyongyang International Airport on his way out of the country.
The man was a former professor at Yanbian University of Science and Technology (YUST), Yonhap said, citing unnamed sources. YUST, a university in neighbouring China, has a sister university in Pyongyang.
An official at South Korea's National Intelligence Service said it was not aware of the reported arrest. Calls to YUST went unanswered.
North Korea, which has been criticised for its human rights record, has in the past used detained Americans to extract high-profile visits from the United States, with which it has no formal diplomatic relations.
North Korea was already holding two Americans.
Otto Warmbier, a 22-year-old student, was detained in January last year and sentenced to 15 years of hard labour by a North Korean court for attempting to steal a propaganda banner.
In March 2016, Korean-American Kim Dong Chul, 62, was sentenced to 10 years hard labour for subversion.
U.S. missionary Kenneth Bae was arrested in 2012 and sentenced to 15 years hard labour for crimes against the state.
He was released two years later.