Pizarro has been a regular for Peru since scoring in a 2–1 defeat against Ecuador on his debut in February 1999. In the same year, he was part of the Peruvian team at the 1999 Copa América in Paraguay, starting all three of the group matches and coming on as a substitute in the quarter-final macth, which ended with a penalty shootout loss against Mexico. Pizarro has gone on to be a starting player at the 2004, 2007 and 2015 Copa América tournaments, as well as the FIFA World Cup qualifying campaigns for the 2002, 2006, 2010, 2014 and 2018.