The 33-year-old mother of three, Ri Hyon Ok, also was accused of spying for South Korea and the United States, and of organizing dissidents, a rights group said in Seoul, citing documents obtained from the North.
The Investigative Commission on Crime Against Humanity report included a copy of Ri's government-issued photo ID and said her husband, children and parents were sent to a political prison the day after her June 16 execution.
The claim could not be independently verified Friday, and there has been no mention by the North's official Korean Central News Agency of her case.
But it would mark a harsh turn in the crackdown on religion in North Korea, a country where Christianity once flourished and where the capital, Pyongyang, was known as the "Jerusalem of the East" for the predominance of the Christian faith.
According to its constitution, North Korea guarantees freedom of religion. But in reality, the regime severely restricts religious observance, with the cult of personality created by national founder Kim Il Sung and enjoyed by his son, current leader Kim Jong Il, serving as a virtual state religion.
The government has authorized four state churches: one Catholic, two Protestant and one Russian Orthodox. However, they cater to foreigners only, and ordinary North Koreans cannot attend the services.
Still, more than 30,000 North Koreans are believed to practice Christianity in hiding - at great personal risk, defectors and activists say.
The U.S. State Department said in a report last year that "genuine religious freedom does not exist" in North Korea.
"What religious practice or venues exist ... (are) tightly controlled and used to advance the government's political or diplomatic agenda," the U.S. Commission on International Religious Freedom said in a May report. "Other public and private religious activity is prohibited and anyone discovered engaging in clandestine religious practice faces official discrimination, arrest, imprisonment, and possibly execution."
Ri, the North Korean Christian, reportedly was executed in the northwestern city of Ryongchon, near the border with China.
"North Korea appears to have judged that Christian forces could pose a threat to its regime," Do Hee-youn, a leading activist, told reporters Friday in Seoul.
The South Korean rights report also said North Korean security agents arrested and tortured another Christian, Seo Kum Ok, 30, near Ryongchon. She was accused of trying to spy on a nuclear site and hand the information over to South Korea and the United States.
It was unclear whether she survived, the report said. Her husband also was arrested and their two children have since disappeared, it said.
The U.S. government commission report cited defectors as saying an estimated 6,000 Christians are jailed in "Prison No. 15" in the north of the country, with religious prisoners facing worse treatment than other inmates.
In Seoul, the rights group said it would try to take North Korean leader Kim to the International Criminal Court over alleged crimes against humanity.
Activists say such alleged crimes; murder, kidnap, rape, extermination of individuals in prison camps; can't take place in North Korea without Kim's knowledge or direction since he wields absolute power over the population of 24 million.