Jacob "Jake" Malone landed at Liberty International Airport in Newark, New Jersey, on Monday afternoon, according to Detective Scott Pezick of the West Whiteland Police Department.
Malone is being held in custody in Essex County and is expected to be brought back to Pennsylvania following an extradition hearing, Pezick said.
A video arraignment in Chester County Prison is expected to follow shortly afterward, he added.
Police in West Whiteland Township, Pennsylvania, allege that Malone, 33, developed a relationship with the alleged victim when she was a minor, then invited her to move in with him and his family, and sexually assaulted her after she turned 18 and was living with them.
Police piece together connection
Police say Malone first met the girl in 2009, when she was 12 and a member of a church in Mesa, Arizona, where Malone was an associate pastor, according to the news release.
A few years later, Malone moved to Minnesota to be a pastor at another church. He contacted the girl, who was 17 at that time, and invited her to stay with his family, according to the release.
"While in Minnesota, the victim alleged that Malone began trying to have inappropriate contact with her," the release says.
In July 2014, the teen moved with Malone, his wife and three children to Pennsylvania, where Malone took a pastor position at Calvary Fellowship Downingtown, a nondenominational church, according to Pezick.
Shortly afterward, the teen told police, he began sexually assaulting her.
The victim, then 18, was given alcohol by Malone, according to Pezick.
On at least one occasion, she was sexually assaulted and impregnated by the pastor, the detective said.
Malone is wanted for rape, sexual assault, endangering the welfare of a child, furnishing liquor to a minor and other related offenses, according to Pezick.
Charles Proctor, Malone's attorney, told CNN he would not comment on the charges at this time, but said he is in daily contact with both the West Whiteland police and Malone, who had been in Ecuador.
Malone went to visit acquaintances in Ecuador in recent weeks as an opportunity to give him and his wife "space," according to Proctor.
Police were expecting Malone to return last week, according to Pezick, but Proctor said it was "logistically impossible" for his client to get the 2 a.m. flight back to the United States.
Fellow pastor: Suspect 'flew completely under the radar'
Malone, Pezick said, "was somebody from the church offering to help her, guide her. And that was the problem. She was looking for guidance and an adult to look up to, and she was taken advantage of."
Malone joined Calvary Fellowship in the summer of 2014. As pastor of leadership development, he was responsible for organizing volunteer teams around the church for programs such as worship and Bible studies, according to Bill Bateman, the church's pastor for global outreach.
"He was very good at it," Bateman said.
The church became aware of allegations against Malone in November 2015, according to Bateman, after they received a call from police detectives in Mesa, where similar allegations had been made against him.
"It was a complete shock. Complete shock," Bateman told CNN.
Supervisors at the church confronted Malone with the allegations shortly after finding out about them, Bateman said. Malone immediately resigned, Bateman added.
"Jake Malone passed every check and participated in every educational forum," the church said in a statement. "He flew completely under the radar, deceiving even those who were closest to him. We know this is hard to imagine, but we assure you that no one suspected anything until very recently."
Bateman said that the situation was "heartbreaking." No other church members have come forward with allegations, he said.
The Police Department in Arizona reached out to Calvary Fellowship after a different woman came to them and said that she was sexually offended by Malone as a minor, according to Detective Esteban Flores of the Mesa Police Department.
That alleged victim, who is now 20, said Malone had "sexual contact" with her beginning in 2009 and continuing until 2011, Flores said.
She was a member of the Trinity Church in East Mesa, where Malone was an associate pastor for youth, Flores said.
The Mesa investigation is ongoing, and charges have not yet been brought in that case, Flores said.
The two women do not know each other, he added.
"We're still waiting for our detectives to get ahold of him and conduct an interview," Flores said. "Our detectives have been in contact with his attorneys. If he returns back to Pennsylvania, we would like to talk to him."