He earned eight caps and scored five goals for the senior team,[9] winning the 2017 FIFA Confederations Cup.

[12] On 10 June 2008, Wagner moved to MSV Duisburg before signing for Werder Bremen on 31 January 2010.

[22][23] He was presented the same day, and took squad number 14, stating: “Hoffenheim are a great club and their ambition impressed me straight away.”[22] He made his competitive debut with the team on 28 August 2016 in the opening Bundesliga matchday against newcomers of RB Leipzig which ended in a 2–2 home draw.

[25] On 31 March 2017, he had his finger dislocated after a clash with Hertha captain Vedad Ibišević, nevertheless he went on to play until the end of the match, also assisting Andrej Kramarić for the third goal in an eventual 1–3 away win.

[31] He opened his scoring account on 27 January by netting the last goal of a 5–2 home win over his former side 1899 Hoffenheim.

[15] Although his contract with Bayern was supposed to expire in 2020, he asked for it to be terminated due to his growing frustrations with his playing time on the pitch.

On 30 January 2019, Wagner transferred to Chinese Super League club Tianjin TEDA for €5 million.

[42] In June 2017, Wagner received his first call-up to the senior national team for a friendly against Denmark and a FIFA World Cup qualifying match against San Marino.

[47] His first and only appearance came on 19 June in the opening Group B match against Australia, missing several good chances to score as Germany won 3–2.

[48] After that, he was benched in favour of Timo Werner and Lars Stindl as Germany defeated Chile 1–0 in the final.

[51] On 16 May 2018, after being left out from Germany's World Cup squad, Wagner announced his retirement from international football.

[59] In June 2023, Wagner became Hannes Wolf's assistant coach at the German U20 national team.

[60] On 10 September 2023, both Wagner and Wolf were named as assistant coaches at the German senior national team to Rudi Völler, who served as interim manager for their friendly against France.

[63] Speaking in June 2017, Germany manager Joachim Löw stated that Wagner had "maturity and personality and one who stands by his own opinion".