The Spaniard has been with Honda since his debut in grand prix racing in 2001, winning the 125cc title in 2003 and 250cc crown in 2004 and 2005.
He made his MotoGP debut in 2006 and has been runner up in the championship three times.
Pedrosa thanked Honda for their trust in him: "It's the best way for me to continue in my racing career, together with the company I was with in my very first race," he said.
Marquez, the youngest ever MotoGP champion at 21, extended his contract for a further two years in May.
(Reporting by Alan Baldwin; Editing by John O'Brien)
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