Ferati moved to Pratteln, Switzerland when he was a child and played for FC Pratteln and FC Concordia Basel as a youth. He signed his first professional contract with Concordia's neighbours, FC Basel, in 2005 and played 28 games for their reserve squad before returning to Concordia during the Summer of 2006. Ferati played for Concordia in the Swiss Challenge League for one and a half years.
In January 2008, he made his way back to FC Basel. Ferati made his Basel debut on 9 February 2008 in the 3–0 home win against Neuchâtel Xamax, but played only five league games during that season. He played in the semi-final of the Uhrencup on 10 Juli 2008. He surprisingly started in their 2–0 UEFA Champions League defeat to Sporting Lisbon at the Estádio José Alvalade as a replacement for the injured François Marque on 1 October 2008 and despite the defeat played as a first team regular from then on. He received very good critics for the Uefa Champions League Group C match on 4 November 2008 in Camp Nou in the 1–1 draw against FC Barcelona.