Stinson, a junior wide receiver, fractured his hip and will have surgery Monday. Jones, a junior cornerback and a third-team punt returner on the STATS FCS Preseason All-America Team, suffered a fractured ankle. He will have surgery later this week.
NCCU lost to FIU 39-14.
"This is very unfortunate for these two young men and their families," coach Jerry Mack said. "Mike is obviously a key player for us and I was looking forward to watching Khalil continue to grow as we enter conference play. We're sure they will be back in 2016 ready to go."
NCCU (1-2) is on a bye week. The Eagles, who won part of a five-way share of the Mid-Eastern Athletic Conference title last season, return to action on Oct. 3 by hosting Bethune-Cookman.