Pedrosa, 29, will miss the MotoGP in the United States on April 12 and the race in Argentina a week later while he recovers from the operation.
Repsol Honda added that test rider Hiroshi Aoyama will temporarily take Pedrosa's place in the team alongside world champion Marc Marquez.
After Friday's operation in Madrid, Pedrosa will have regular checkups with surgeon Angel Villamor in the coming weeks and then begin a custom physiotherapy programme.
"A recovery time of four to six weeks is expected, however, his return to racing won’t be confirmed until Dr. Villamor can ascertain the success of the surgery," Repsol Honda said.
Pedrosa is suffering from a problem common among motorcycle racers. Pressure builds up in the forearm, causing intense pain, and makes riding a bike difficult when the muscle becomes too big for the 'sack' that it sits in.
Pedrosa, whose compatriot Marquez has won the last two championships, has not won a MotoGP race since the Czech Grand Prix last August and was sixth in the season-opener in Qatar last weekend.
(Reporting by Iain Rogers, editing by Pritha Sarkar)
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