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 programs 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.
"It's also a resolve to point a double-action revolver against the US and China because he is a US citizen who worked in China."
US President Donald Trump has urged China to take stronger steps to press the North to curb its nuclear and missile programms.
Trump's deputy Mike Pence, during a regional tour last week, warned that "all options are on the table" to curb the North's nuclear ambitions as fears grow it may be planning another atomic test.
Two other US citizens — college student Otto Warmbier and Korean American pastor Kim Dong-Chul — are currently being held in the North after being sentenced to long prison terms.
Kim was sentenced last year to 10 years' hard labor for spying.
Also last year Warmbier was jailed for 15 years for stealing a propaganda sign and for "crimes against the state".
The North has arrested and jailed several US citizens in the past decade, often releasing them only after high-profile visits by current or former US officials.