The potential inclusion of both players, who have already established themselves in Fabio Capello's senior squad, had been controversial.
Carroll, who became the most expensive English player in January, has suffered with injuries during the second half of the season, while Wilshere has started more than 40 games for his club this season.
"Andy Carroll and Jack Wilshere will not be part of the under-21 squad which travels to Denmark. Andy has been ruled out through injury," Pearce said in a statement on the Football Association website.
"I spoke to Jack last week and he explained that while he told me in March that he wanted to be part of the squad, he now feels he is not in the best condition to take part in the finals.
"That is based on the number of games he has played for Arsenal this season, sports science data which Jack was presented with last week and concerns he has for his fitness looking ahead to next season."
Carroll has been dogged by injury since he completed a 35-million-pound move to Liverpool in January and has started only five league games for the club.
Wilshere, however, has been almost ever-present for Arsenal this season and club manager Arsene Wenger said last week England would be gambling with his health by calling him up for the June 11-25 tournament.
"Jack has always expressed his enjoyment at being involved with the under-21 squad, and while I am disappointed not to have him with us for the finals I've accepted the situation," Pearce added.
