It is unclear what injury he has, but the Football Association said he had suffered it while playing for Celtic in Sunday's CIS Cup final loss to Rangers at Hampden Park.
The U21 squad will take on Denmark in Viborg on Friday night, before hosting Iceland at Deepdale on Monday.
Hooper is one of five players who have withdrawn from the squad, including former Iron loanee Henri Lansbury.
Jack Rodwell, Mark Davies and Alex Smithies have also pulled out of the games, which will serve as warm-ups for the European Championship this summer.