Nagatomo started his second Inter Milan season by playing 62 minutes in the opening Serie A match against Palermo, ended in a 4–3 away defeat. On 27 September 2011, Nagatomo provided an assist for Giampaolo Pazzini by nutmegging Aleksei Berezutski before driving the ball across goal during the 3–2 away win against CSKA Moscow in the second group stage match of Champions League. He scored his first goal of the season on 10 December 2011 during the 2–0 home win against Fiorentina in the matchday 15 of Serie A. He was again in the scoresheet three days later as he headed home a Ricky Álvarez cross in the 1–0 win against Genoa. In the last match of 2011 against Lecce at home, Nagatomo produced a "man of the match" performance by providing two assists in an eventual 4–1 win.