In his first season as a Shakhtar player he played 34 matches, including 23 league appearances, and scored three goals, with one coming in the league. Shakhtar were victorious in the Super Cup, however Fernandinho did not play in the match. He played in the championship deciding match between Shakhtar and Dynamo Kyiv, who were level on 75 points after all 30 games had been played, in which Shakhtar prevailed 2–1 to take the title. This marked Fernandinho's first league title with Shakhtar. He made 25 league appearances in the 2006–07 season as Shakhtar finished 2nd to Dynamo Kyiv. They also finished as runners-up in the Ukrainian Cup and Ukrainian Super Cup.