The Unification Ministry said the fisherman had been rescued June 16 while drifting in a damaged squid boat in South Korean waters.
"He said he had no intention to return to North Korea," ministry spokesman Kim Eui-Do said, underlining Seoul's policy of only repatriating those fishermen who ask to be sent home.
It's the latest in a series of cases involving rescued North Korean fisherman which have triggered angry exchanges between Seoul and Pyongyang.
Five fishermen who opted to return were repatriated a week ago at the border truce village of Panmunjom.
Hundreds of North Koreans flee their isolated homeland each year.
Most cross into China and then to a third country such as Thailand before coming to the South. Intentional defections across the sea or land border between the two Koreas are rare.