Hwang Seon, a unification activist who rose to prominence in 2005 when she had a baby in Pyongyang, was taken into custody early on Wednesday, said a prosecution official who asked not to be identified.
The prosecution official said a Seoul court granted a request on Tuesday to detain Hwang on charges of breaking the National Security Law. Hwang denied the charges as she entered the court for a hearing.
The law, enacted after the two Koreas were split at the end of World War Two but before the 1950-53 Korean War, prohibits South Koreans from publicly praising the North Korean regime.
It is considered obsolete by liberal critics, who say it is often used by conservative governments to stifle political opposition and suppress freedom of speech.
South Korean President Park Geun-hye said on Monday the law was still needed as a way to protect South Korea from the North, with which it technically remains at war under a truce that suspended fighting in the Korean War.
Immigration authorities deported a Korean-American woman to the United States on Saturday for making positive comments about life in the North, a potential violation of the same law, as well as immigration laws.
Shin Eun-mi, a South Korea-born American who came to the South last year as a tourist, had spoken positively of life in North Korea in speeches around the country, some with Hwang, as well as in online posts.
Shin blamed South Korea's news media for encouraging alienation between the two Koreas.