The forward follows defender Connor Teale in making the move from the Premier League club to Highbury, both having signed contracts at Fleetwood for the next two seasons, with options of a further year.
McMillan has featured 14 times in the Under-18 Premier League this season, also playing in the FA Youth Cup, EFL Trophy and Premier League 2.
The York-born teenager, who is also eligible to represent South Africa through his father, will join up with Stephen Crainey’s development squad at Poolfoot Farm.
Ryan Rydel left Fleetwood for Stockport County this week, while forward Harvey Saunders was loaned to their National League rivals Hartlepool United.
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