Officially, the church said its decision to sever ties stemmed from the fact that it has now grown into a worldwide organisation, with many members outside of the United States.
The church said it wants to explore global youth programs that can serve its members outside the U.S.
Individual Mormons who wish to remain part of the Scouts will simply be integrated into regular troops. It ended its ban on openly gay youths participating in its activities in 2013 and ended its ban on openly gay adult leaders two years later.
Last year, the church ended its participation in the Boy Scout programs for teenagers.
The relationship the Boy Scouts have with the Mormon Church is stronger than with any other religious group.
The church has been the BSA's largest faith-based chartering organization and LDS boys have comprised about 1 in 6 Scouts.
The Boy Scouts and LDS have been partners for a century. Last year, the church already pulled 185,000 members over the age of 14 from the Scouts - a significant number - though the Boy Scouts claim to have over 2.4 million youth members.
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Church officials did not cite specific Scouts policy changes that spurred the split, but the two groups have increasingly clashed over values in recent years, particularly following the Boy Scouts' move to include openly gay troop leaders.
"We have jointly determined that, effective on December 31, 2019, the Church will conclude its relationship as a chartered organization with all Scouting programs around the world", it concluded.
Last October, the BSA announced that girls would be allowed to join their organization, a move that drew criticism from many groups. The Cub Scouts program, for children ages 5-10, will not undergo a name change.
In a separate statement, the Boy Scouts of America said it is "confident that many LDS Scouting families will go on to enjoy Scouting for years to come".
As the Mormon Church leaves the Boy Scouts, there will be a loss in funding.
The Mormon church was the Boy Scouts' first scouting sponsor in the United States.