On 17 May 2017, Werner was named in Germany's squad for the 2017 FIFA Confederations Cup held in Russia. He appeared as a substitute for Sandro Wagner in the team's opening game of the tournament against Australia, before scoring his first two international goals when selected to start in Germany's final group match against Cameroon on 25 June. Four days later, Werner scored Germany's third goal in a 4–1 semi-final victory over Mexico. On 2 July 2017, Werner assisted Lars Stindl's tournament winning goal in the 2017 FIFA Confederations Cup Final against Chile. With three goals and two assists, Werner was awarded the tournament's Golden Boot.