Dana 11. lipnja 2016. godine, Werner je potpisao četverogodišnji ugovor s [[RB Leipzig]]om. Transfer je iznosio 10 miljuna eura čimete je učinilo Werner postao najskuplje pojačanje u povijesti RB Leipziga.<ref name=":4" /> Dana 26. rujna 2016., na utakmici protiv [[1. FC Köln|Kölna]], kada je bio star 20 godina i 203 dana, postao je najmlađi igrač u povijesti Bundeslige sa 100 nastupa u toj ligi.<ref name=":5">{{Cite web|url=https://www.bundesliga.com/en/news/Bundesliga/blmd5n-timo-werner-becomes-youngest-member-of-bundesliga-100-club.jsp|title = RB Leipzig {{!}} Werner becomes youngest member of Bundesliga 100 club {{!}} bundesliga.com|website=bundesliga.com - the official Bundesliga website|language=en|access-date = 19 May 2018}}</ref> Tako je oborio rekord koji je prethodno držao [[Julian Draxler]] koji je u vrijeme postavljanja rekorda bio stariji za 22 dana.<ref>{{Cite news|url=http://kwese.espn.com/football/rb-leipzig/story/2959491/rb-leipzigs-timo-werner-is-youngest-to-play-100-bundesliga-games|title = Werner breaks 100-game age record|work=ESPN.com|access-date = 19 May 2018}}</ref> Werner je završio sezonu 2016./17. s 21 golom, čime je postao najbolji strijelac te sezone Bundeslige te je također pomogao Leipzigu da prvi put u klupskoj povijesti ostvari plasman u [[UEFA Liga prvaka|UEFA Ligu prvaka]].<ref>{{Cite news|url=https://theworldgame.sbs.com.au/werner-s-originals-give-germany-striking-solution|title = Werner's originals give Germany striking solution {{!}} The World Game|work=The World Game|access-date = 19 May 2018|language=en-GB}}</ref><ref>{{Cite news|url=https://www.dfb.de/en/news/detail/a-brace-each-for-werner-and-selke-as-leipzig-reach-the-champions-league-166945/|title = A brace each for Werner and Selke as Leipzig reach the Champions League|work=DFB - Deutscher Fußball-Bund e.V.|access-date = 19 May 2018|language=en}}</ref>
U ožujku 2018. godine, u utakmici protiv bivšeg kluba Stuttgarta, postao je najmlađi igrač sa 150 nastupa u Bundesligi, srušivši rekord koji je prethodno držao [[Charly Körbel|Karl-Heinz Körbel]].<ref name=":6">{{Cite web|url=https://www.bundesliga.com/en/news/Bundesliga/timo-werner-rb-leipzig-150-bundesliga-games-stuttgart-manchester-united-liverpool-475363.jsp|title = RB Leipzig's Timo Werner makes Bundesliga history, back where it all began at Stuttgart {{!}} bundesliga.com|website=bundesliga.com - the official Bundesliga website|language=en|access-date = 19 May 2018}}</ref> Kasnije tog mjeseca pomogao je Leipzigu pobijediti [[FC Bayern München|Bayern Münchenu]] po prvi put, kada je zabio pobjednički gol (2:1).<ref>{{Cite news|url=https://www.si.com/soccer/2018/03/18/rb-leipzig-2-1-bayern-munich-timo-werner-shines-red-bulls-upset-german-giants|title = RB Leipzig 2-1 Bayern Munich: Timo Werner Shines as Red Bulls Upset German Giants|work=SI.com|access-date = 19 May 2018|language=en}}</ref>
