Kimmich started the 2016–17 season by coming on as a substitute in a 2–0 win against Borussia Dortmund in the 2016 DFL-Supercup. On 9 September, he scored his first goal for FC Bayern in a 2–0 Bundesliga, away win at FC Schalke 04. Four days later, he scored his first two Champions League goals in a 5–0 home win against FC Rostov. Kimmich scored a late winning goal in the 88th minute in a 1–0 away victory over Hamburger SV. He finished the 2016–17 season with nine goals in forty appearances.