Two days after being granted free agency, Navarro signed with the Chicago Cubs. Navarro started in 29 games for the Cubs that year, and posted much-improved numbers on the season. He led the team in many pitching categories that year, such as wins and innings pitched. Navarro was granted free agency on November 1, but on December 8, , he accepted the Cubs' salary arbitration offer, and then agreed to a $3.4 million contract for the season. Navarro led the team again in 1996 with a 15–12 record, 3.92 earned run average, four complete games and 158 strikeouts. Oddly enough, Navarro also led the league in batters faced and hits allowed. On October 28, , Navarro was again granted free agency by the Cubs and he signed to a four-year, $20 million contract with the crosstown rivals of the Cubs, the White Sox, on December 11.
