The 28-year-old is coming off his best season, recording career-highs in batting average (.288), on-base percentage (.347), home runs (nine), triples (five) and runs scored (34) through 82 games.
"Nick has developed into one of our club's core players," Padres executive vice president and general manager Josh Byrnes said. "He impacts the game on both offense and defense and has evolved into a leader on the field and in the clubhouse."
San Diego selected Hundley in the second round of the 2005 draft and he has appeared in 305 games with the Padres since 2008. He is a career .255 hitter with 56 doubles, 30 home runs, 126 RBI and 111 runs scored.