Matthew Bowman, a Mormon scholar and history professor at Henderson State University, said the split reflects the two organizations' diverging values.
"The church is wedded very much to traditional gender roles and they see the Boy Scouts of America increasingly move away from that," Bowman told CBS News. "That means that they have come to see it as less of a hospitable place.”
KUTV reported that the church did not believe boys between 14 and 18 are “being served well” by the Varsity or Venturing programs.
The Mormon church has been involved in scouting for more than a century.
Boy Scouts of America spokeswoman Effie Delimarkos said the organization is saddened by the decision but understands the church's desire to customize a program, CBS News reported.
In a statement, the Boy Scouts of America said it “deeply appreciates” its relationship with the church.
“We recognize that not all programs are a perfect fit for all partners," the statement said.
About 280,000 Mormon boys ages 8 to 13 will remain in the Scouts while the church develops its program, church officials said.
Jana Ockey has three boys who all got their Eagle Scout awards when they were 13 years old, KUTV reported. Two of them, Justin, 16, and John, 14 are now in the Varsity and Venturing program.
"I felt like there was a death. It was that strong for me," Ockey told KUTV. "I've been in the scouting program for so long and when I saw what the venturing program could do for the boys I thought it was amazing. The frustration was, not everybody could see that."
For those boys who still wish to work toward an Eagle Scout badge, the church told KUTV they will be “registered, supported and encouraged.”