Mustoe is regarded as an exciting prospect for the future by the Latics but has yet to establish himself in Roberto Martinez's first team.
He has already had spells out on loan with Barnet and Morecambe and has now been sent to gain further experience in the lower leagues.
A deal was agreed on Thursday for the 22-year-old to head to Brunton Park, where he will provide another defensive option for Greg Abbott.
Abbott told Carlisle's website: "Jordan is one we've been talking about for a while now and it's good for us that we've got him in.
"He's had a couple of good, long loan spells before this one, where he has done very well, and he's very highly thought of at Wigan.
"He adds more options to the squad and it should help us with the work we have been doing defensively over the last couple of months.
"It's a great opportunity for him to come in and get some competitive football at an age when that's exactly what he wants and needs.
"As always in these cases, if it goes well, as we think it will, then it's a good move for all concerned."
The Cumbrians are currently 16th in League One after a promising recent run which has seen them beaten just once in six games.