The 21-year-old midfielder will remain at the Trotters for the remainder of the current season.
A Republic of Ireland youth international at various levels, Charsley made his first-team debut for Everton during their 3-0 win over Apollon Limassol in this season's Europa League.
"Harry is a player we have watched a lot and he can play all across the midfield as well as in behind the striker," Bolton manager Phil Parkinson told the club's website.
"He's from Everton's Under-23 team where a lot of their players have gone out on loan and have done well with the help of David Unsworth and his team.
"They almost play like a league team, so when you get a player from Everton's youth ranks, you know that they are ready and are hardened to understand the rigours of what it takes to win games of football."
Charsley will go straight into the Bolton squad for this week's match against Brentford.