After becoming Leipzig's all-time top goalscorer, Werner departed to Chelsea in 2020 for a reported fee worth €50 million, winning the UEFA Champions League in his first season at the club.

[7] Werner made his senior debut later that year in a 2013–14 UEFA Europa League qualifying phase match against Botev Plovdiv.

[7][9] Upon doing so, he became the youngest player to ever play in an official match for Stuttgart at the age of 17 years, four months and 25 days, breaking the record previously held by Gerhard Poschner.

[15][16] On 11 June 2016, Werner agreed to a four-year contract with RB Leipzig for a reported transfer fee of €10 million, the largest in the club's history.

[19][20] Werner ended the 2016–17 Bundesliga season with 21 goals, making him the leading German goalscorer in the division, and helped RB Leipzig qualify for the UEFA Champions League for the first time in the club's history.

[21][22] In a match against his former club Stuttgart in March 2018, Werner became the youngest player to reach the milestone of 150 Bundesliga appearances, eclipsing the record previously held by Charly Körbel.

[35] On 18 June 2020, Werner agreed to sign for Premier League club Chelsea, who activated his £47.5 million release clause, on a five-year contract.

[38] On 29 September, Werner scored his first goal for Chelsea in a 1–1 draw against Tottenham Hotspur which they lost 4–5 on penalties in the fourth round of the EFL Cup.

[39] On 17 October, Werner scored his first Premier League goals with a brace and assisted Kai Havertz for the third as Chelsea drew Southampton 3–3 at home.

[44] Werner started the 2021–22 season in the 2021 UEFA Super Cup match against Villarreal on 11 August 2021, and following a 1–1 draw after extra time, Chelsea won the penalty shoot-out 6–5.

[47] On 8 December 2021, Werner scored the fastest goal for Chelsea in their Champions League history, after only 82 seconds away to Zenit Saint Petersburg.

He also scored, firing a dipping shot from outside the box at Köln goalkeeper Marvin Schwäbe, who let it slip through his hands to give Leipzig the opener in the 36th minute.

[52] On 2 November 2022, Werner suffered an ankle injury and had to be substituted in Leipzig's 4–0 Champions League victory over Shakhtar Donetsk, which saw him ruled out of the 2022 FIFA World Cup in Qatar for Germany.

[58][59] Later that year in late May, Tottenham extended Werner's spell for a season-long loan with an option to buy clause in the region of £8.5 million.

[60] Werner scored his first goal of the 2024–25 season on 30 October in the fifth minute during a League Cup tie against Manchester City, which Tottenham went on to win 2–1 to advance to the quarterfinals.

[13] Werner was called up to the German senior squad in 2017 by head coach Joachim Löw for the friendly against England and the 2018 World Cup qualification match against Azerbaijan on 22 and 26 March 2017 respectively.

He appeared as a substitute for Sandro Wagner in the team's opening game of the tournament against Australia,[63] before scoring his first two international goals when selected to start in Germany's final group match against Cameroon on 25 June.

[65] On 2 July 2017, Werner assisted Lars Stindl's tournament winning goal in the 2017 FIFA Confederations Cup Final against Chile.