Stones was initially linked with York yesterday afternoon, with manager Adam Hinshelwood refusing to rule out a potential move for the striker.
The club have now confirmed his capture for an undisclosed fee.
Stones was initially a product of the Guiseley academy, with former FA Cup winners Wigan Athletic snapping him up in 2022.
Since joining Wigan, Stones had struggled to nail down a regular spot in the first-team, instead spending a stint on loan to Scotland with Ross County.
Upon his return to England, Stones joined Oldham Athletic for his first spell, impressing with three goals in four matches for the Latics.
He also appeared on the bench in Wigan’s win over City in last season’s FA Cup encounter.
Stones returned to Oldham and the National League for a brief spell this season, and again impressed, with four goals in six matches.
The 21-year-old was recalled by Wigan, with the League One side hopeful of cashing in on their prospect.
York have won the race for the striker, with reports of interest from the Football League.
Stones will be unavailable to make his debut for City in this afternoon’s FA Trophy match at Gainsborough Trinity (3pm) due to being cup-tied.
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