Pereira signed for Inter Milan in late August 2012 for €10 million on a four-year contract, reuniting with former Porto teammate Fredy Guarín. He made his Serie A debut on 2 September in a 1–3 home loss against A.S. Roma, and finished his first season with 40 appearances all competitions comprised, scoring his only goal in a 2–0 league victory at A.C. ChievoVerona.