In December 2016, Pachuca announced Pizarro was transferred to Guadalajara for a reported $15 million, in a deal that saw Víctor Guzmán go the other way, permanently joining Pachuca. On 7 January 2017, Pizarro made his debut against Club Universidad Nacional, playing the whole match in which Guadalajara won 2–1. A week later, Pizarro scored his first goal for Guadalajara against Monterrey from a long range shot, the game ended 2–2.
On 7 July 2016, Pizarro was named in Mexico's 18-man squad that would participate in the 2016 Summer Olympics in Rio de Janeiro, Brazil. In Mexico's first group stage match against Germany, he scored Mexico's second goal to make the game 2–1 but was eventually tied 2–2. In Mexico's second group stage match against Fiji, Pizarro along with teammate Oribe Peralta, would pick up injuries. They were subsequently replaced by Carlos Fierro and Raúl López Gómez.