The Madchester band, who reformed last October, have this year sold out their first tour since 1995.
Speaking to NME, Eavis commented: "I would like them to come back at some point.
"Are they a possible headliner for next year? I think it is possible, yeah."
Teasing next year's festival, Eavis added: "There's not a shadow of a doubt - it will be the best festival we've ever done."
The Arctic Monkeys' Alex Turner said last year that he would like a second shot at headlining Glastonbury.
Earlier this month, it was reported that the Roses were preparing to release a new album, possibly their third after 1994's Second Coming.
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Watch The Stone Roses perform 'I Wanna Be Adored' at this year's Benicassim Festival below: