The 2009–10 season saw Shakhtar lift the Premier League trophy. Fernandinho's first goal came on 29 July, in a 2–2 Champions League draw against Politehnica Timișoara in the third qualifying round, however Shakhtar were knocked out of the competition, losing on away goals after a 0–0 draw at home. On 20 September, he scored a penalty in a 4–2 victory over Arsenal Kyiv. He scored two goals in a 5–1 victory over Karpaty Lviv on 18 October, including one from the penalty spot. On 22 October the first goal, a penalty, in a 4–0 victory against French side Toulouse in the Europa League. He scored a 93rd-minute goal in a 2–0 Ukrainian Cup victory against Dynamo Kyiv on 28 October. On 6 December he scored a penalty to open the scoring in a 2–0 win over Kryvbas. On 24 March, he scored a 92nd-minute goal against Metalurh Donetsk in the Ukrainian Cup, however it proved to be only a consolation goal as Shakhtar lost the match 2–1. Fernandinho made 24 league appearances, netting 4 times. He made a total of 39 appearances with 8 goals.