The 21-year-old Republic of Ireland Under-21 international has signed an initial two-year deal with the Latics, with the option of a further 12 months.
Duffus did not make a senior appearance for Everton but helped their under-23 side win Premier League 2 last season.
He previously had a loan spell with Bury in 2014, making five appearances for the Shakers.
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League One side Oldham Athletic have signed striker Courtney Duffus from Everton for an undisclosed fee.