 In the first round of the UEFA Cup, Fernandes made his European Cup debut for Sion in a 0–0 draw against Bayer Leverkusen and in the second round of UEFA Cup, Fernandes scored his first professional league goal and first European Cup goal against Leverkusen which Sion lost 3–1 on aggregate.On 14 October 2006, Fernandes scored his first league goal for Sion in a 1–1 draw against Luzern.Fernandes also led his team win the Swiss Cup in a penalty shootout (5–3) against Young Boys.