Victor Arden Barnard, 53, was arrested Friday at a home in a gated community, said the Public Security Secretariat of Rio Grande do Norte state. A 33-year-old woman was detained, police said.
Both were transported to a federal jail in Lagoa Nova in Natal, awaiting extradition to the United States, authorities said.
Barnard is suspected of 59 counts of sexual assault in Minnesota. He is accused of sexually abusing two young girls who were members of his church, the U.S. Marshals Service said.
The last U.S. sighting of Barnard was last year in Raymond, Washington. The fugitive was featured on CNN's "The Hunt With John Walsh"
last year and again last week.
Barnard was featured on the U.S. Marshal's 15 Most Wanted List along with a $25,000 reward for information leading to his arrest. In addition to the sexual assault allegations, he was also wanted for unlawful flight to avoid prosecution.
As a pastor, Barnard inspired his congregants with his charisma and apparent devotion to the teachings of Jesus Christ.
"I had never met anybody that I thought loved the word of God as much as Victor Barnard did," said Ruth Johnson, a former member of Barnard's River Road Fellowship.
Barnard set up a so-called "shepherd's camp" in the mid-1990s in Pine County. Several congregants moved to the rural area about 100 miles north of Minneapolis to be a part of the camp.
In June 2000, the pastor allegedly convinced some members of his congregation to hand over their firstborn daughters to live with him in a secluded campsite.
Lindsay Tornambe's name was called, and her parents allowed their 13-year-old daughter to join the group of girls at the camp, called "The Maidens," under Barnard's supervision. She and other congregants said the girls got up early, sewed, cooked and cleaned.
"Everything that a wife would do, they did for him," Johnson said.
Barnard proclaimed he was Christ on Earth.
"He taught that in the Bible, the church was the bride of Christ and because he was Christ in the flesh, the church was supposed to be married to him," Tornambe said. "At that time, I didn't really understand the fullness of what it meant."
The complaint filed in Minnesota says Tornambe alleges she was sexually abused by Barnard from the ages of 13 to 22 while she and her parents were members of River Road Fellowship. She told investigators the group of 10 young girls and women were known as Alamoths, or maidens. Her group was sent to what she thought was a summer camp, the document says.
Tornambe told investigators Barnard sexually assaulted her one to three times a month until she left in 2010 to be with her parents, who had moved to Pennsylvania.
In fall 2011, Tornambe was contacted by another former maiden who shared a similar story: She said she was molested by Barnard from the time she was 12 until she was 20, although she said the number of sexual acts varied each month.
Tornambe and the other woman went to the police in Minnesota. Barnard had moved to Washington state after an admission to affairs with married women caused the religious group to split, the complaint says.
The ministry operated in a secluded area of Pine County from about 2000 until 2011 or 2012, Chief Deputy Steven Blackwell of the county sheriff's office told CNN last year.
The fellowship left the property shortly after a new sheriff was elected and began investigating the ministry, Blackwell said. Afterward, The Salvation Army started running a family camp there.