Pedrosa, 29, will go under the knife in Madrid on Friday, with an estimated recovery period of four to six weeks, meaning he will definitely miss the MotoGP in the United States on April 12 and the race in Argentina a week later, Repsol Honda said.
Test rider Hiroshi Aoyama will temporarily take Pedrosa's place in the team alongside world champion Marc Marquez, they added.
Pedrosa is suffering from a problem common among motorcycle racers. Pressure builds up in the forearm, causing intense pain, and makes riding a bike exceptionally difficult when the muscle becomes too big for the 'sack' that it sits in.
"Obviously this isn't the news I wanted to be sharing with everyone," said Pedrosa.
"However, after speaking with some key doctors and medical professionals that I trust, they are all in agreement that this is the only option for me.
"We will have the surgery on Friday and they will use a special technique to help close the wound to try and prevent this issue continuing to affect me."
Pedrosa, whose compatriot Marquez has won the last two championships, has not won a race since the Czech Grand Prix last August.
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