On 15 July 2008, Fernandinho played in the Super Cup victory against Dynamo Kyiv. The match went to penalties after the two teams drew 1–1 at the end of extra time. Fernandinho scored one of the penalties to help Shakhtar to a 5–3 win in the shoot-out. He scored the equalising goal in a 1–1 draw with Karpaty Lviv on 27 July. On 3 August he picked up a 63rd minute red card in a 3–0 victory over Illichivets Mariupol. On 31 August he scored a penalty in a 2–2 draw against Metalurh Zaporizhya. On 16 September he scored the opening goal in a 2–1 Champions League victory against Swiss club Basel. On 8 November, he scored the opening goal in a 2–0 victory against Tavriya Simferopol. On 9 December he scored a goal in Shakhtar's 3–2 away win against Spanish side Barcelona in the Champions League group stage match.