Nagatomo was born in Saijo on September 12, 1986. When he played for Meiji University, he also played for FC Tokyo in 2007. After graduating from the university, he joined FC Tokyo in 2008. He became a regular left side back from first season. The club won the champions in the 2009 J.League Cup. In summer 2010, he moved to Italian Serie A club Cesena. In January 2011, he moved to Internazionale Milano. He played 170 matches for the club in 7 seasons. In February 2018, he moved to Turkish Süper Lig club Galatasaray. The club won the champions in the 2017/18 and 2018/19 season. In summer 2020, he moved to French Ligue 1 club Olympique Marseille.