"I am sad and disappointed to announce that I will not be able to participate in Wimbledon this year," the Australian Open champion said in a statement on Tuesday.
Question marks over the Belgian's health were raised after she was knocked out in the second round of the French Open last month.
Before arriving in Paris to defend her Roland Garros crown, Henin-Hardenne had not played a tournament since early April having suffered from a viral infection.
"My physicians have given me strict orders that several more weeks of rest are necessary to ensure a full recovery," Henin-Hardenne
"Since the day I walked off the court after the semi-finals at Wimbledon last year, I have been looking forward to competing on the grass again. Unfortunately, my dream of holding the Wimbledon trophy must wait another year. I look forward to an early and complete recovery."
Her fellow Belgian, world number two Kim Clijsters, withdrew from the tournament on Monday with a wrist injury.