Boon, 19, has made three first team league appearances for Bolton.
He spent a part of last season at Northwich Victoria, where he played with Atherton manager Brad Cooke.
“The loan came about with Brad being my captain at Vics," Boon said.
"He saw my potential there when playing with him, he liked the way I played with confidence and looking to start things off from the back to build the attack.
“My objectives are to come and enjoy my football and get playing time, and to also experience a different league and the style of play to test myself, I also look to aim to get Colls up the table and hopefully make the play offs, I can’t wait to get started."
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