Dana 18. lipnja 2020. Werner je pristao potpisati petogodišnji ugovor s [[Chelsea F.C.|Chelseajem]] koji je aktivirao njegovu otkupnu klauzulu od 47,5 milijuna funti. Pridružio se klubu 1. srpnja.<ref>{{cite web |url=https://www.bbc.co.uk/sport/football/53092225 |title=Timo Werner: Chelsea agree to sign forward from RB Leipzig on five-year deal |website=BBC Sport |date=18 June 2020 |access-date=18 June 2020}}</ref> Trinaest dana kasnije debitirao je za Chelsea u utakmici [[FA Premier liga|Premier lige]] protiv [[Brighton & Hove Albion F.C.|Brighton & Hove Albiona]] (3:1).<ref>{{cite web |url=https://www.skysports.com/football/news/11668/12071888/timo-werner-gives-chelsea-new-dimension-in-win-over-brighton |title=Timo Werner gives Chelsea new dimension in win over Brighton |website=Sky Sports |date=15 September 2020 |access-date=15 September 2020}}</ref> Dana 29. rujna postigao je svoj prvi gol za klub u utakmici 4. runde [[FAEngleski Liga kup|Lige kupa]] protiv [[Tottenham Hotspur F.C.|Tottenham Hotspura]] koju je Tottenham dobio 5:4 na penale (prije penala bilo je 1:1).<ref>{{cite web |url=https://www.goal.com/en-in/match/tottenham-hotspur-v-chelsea/sagg9rj0febpb8zztm0shm38 |title=Tottenham 1-1 Chelsea (5-4 pens): Werner off the mark but Mount miss sends Spurs through |website=Goal |date=30 September 2020 |access-date=30 September 2020}}</ref> U utakmici protiv [[Southampton F.C.|Southamptona]] odigrane 17. listopada, zabio je svoja prva dva gola u Premier Ligi te je asistiro [[Kai Havertz|Kaiju Havertzu]] za treći (3:3).<ref>{{cite web |url=https://www.goal.com/en/news/werner-50-per-cent-happy-first-premier-league-goals-chelsea/8fg3v4vs5dfx1il25n75xdqg8 |title=Werner left 50 per cent happy with first Premier League goals as Chelsea throw two points away |website=Goal |date=17 October 2020 |access-date=17 October 2020}}</ref> Jedanaest dana kasnije zabio svoj prvi gol u [[UEFA Liga prvaka|UEFA Ligi prvaki]] za Chelsea i to [[FK Krasnodar|Krasnodaru]]..<ref>{{cite web |url=https://www.chelseafc.com/en/news/2020/10/29/timo-werner-reflects-on-resilience-shown-to-withstand-pressure-a |title=Timo Werner reflects on resilience shown to withstand pressure and penalty-taking options |publisher=Chelsea F.C. |date=29 October 2020 |access-date=29 October 2020}}</ref>
