Hughes has been fighting a stomach virus, but his health is improving enough that the Yankees are comfortable giving him the ball for Thursday's game.
"He feels better," Yankees manager Joe Girardi said. "If he doesn't feel good enough to make his start, it will be Nova."
Girardi said that the plan is to have Nova, who was scheduled to pitch on Wednesday, available to pitch out of the bullpen for a few days and then slot him in to rejoin the rotation next week.
"I know that CC [Sabathia] and Co. have to pitch every five days," Nova said. "I understand that part, and I've just got to be ready when they tell me to go out there.
"I feel really good when my day to pitch is coming. All I want to do is go out there and pitch. Now I've got to wait five more days. It's going to be like, for me, a month."
The Indians were scheduled to pitch Corey Kluber on Wednesday, and are planning to start Zach McAllister as originally scheduled in Thursday's game.
Girardi said that he did not want to push his rotation back because Monday's off-day would create a scenario where Andy Pettitte would receive seven days of rest. Girardi acknowledged that Thursday's forecast for the Cleveland area is also ugly.
"We're going to probably get banged tomorrow too," Girardi said. "Hopefully we don't."
It is possible that the Yankees could travel back to Cleveland on May 13, originally scheduled as an off-day following a series in Kansas City, to make up Wednesday's rainout. That plan has not been finalized.
Bryan Hoch is a reporter for MLB.com. Follow him on Twitter @bryanhoch and read his MLBlog, Bombers Beat. This story was not subject to the approval of Major League Baseball or its clubs.