There was no immediate official confirmation of the reported arrest, which would come at a tense time in relations between Pyongyang and Washington.
Yonhap quoted sources as saying the man, identified only by his surname Kim, was arrested last Friday at Pyongyang International Airport on his way out of the country.
It said Kim, aged in his late 50s and a former professor at China's Yanbian University of Science and Technology, had been involved in aid programmes for the North.
He reportedly was in the North for about a month to discuss relief activities, Yonhap said. The reason for his arrest was unclear.
South Korea's National Intelligence Service and the unification and foreign ministries said they could not confirm the report.
But the director of a Seoul-based group called the World North Korea Research Center said his sources in Pyongyang had confirmed the arrest.
"The reason North Korea is not saying anything yet is because it is not done with the investigations," Ahn Chan-il, a former defector, told AFP.
"It is important for them to hold a US citizen hostage at this point to prevent Washington from carrying out a decapitation of Kim Jong-Un," Ahn said, referring to the North's fears that the US plans a secret military strike to topple its leader.
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