Za razliku od prethodnih godina, nije nastupio ni na jednom turniru prije [[Australian Open 2013 – muški singl|Australian Opena]]. U Melbourneu je u prva četiri kola pobijedio [[Benoît Paire|Pairea]], Davidenka, [[Bernard Tomić|Tomića]] i Raonića, ne izgubivši nijedan set ili servis-gem i plasiravši se tako u 35. uzastopno četvrtfinale na Grand Slam turnirima (niz je počeo na Wimbledonu 2004).<ref>{{cite web |url= http://www.atpworldtour.com/News/Tennis/2013/01/4/Australian-Open-Monday-Federer-Beats-Raonic.aspx |archiveurl= https://web.archive.org/web/20140806160433/http://www.atpworldtour.com/News/Tennis/2013/01/4/Australian-Open-Monday-Federer-Beats-Raonic.aspx |title= Federer Topples Raonic To Reach 35th Successive Major QF|archivedate=6. 8. 2014|publisher=ATP World Tour|accessdate=16. 6. 2015}}</ref> AliNo, zato ga je u četvrtfinalu dobro namučio Tsonga. Meč je trajao tri i po sata, a Federer je na kraju slavio sa 7–6<sup>4</sup>, 4–6, 7–6<sup>4</sup>, 3–6, 6–3.<ref>{{cite web|url=http://www.atpworldtour.com/News/Tennis/2013/01/4/Australian-Open-Wednesday-Federer-Edges-Tsonga.aspx|archiveurl=https://web.archive.org/web/20131226102358/http://www.atpworldtour.com/News/Tennis/2013/01/4/Australian-Open-Wednesday-Federer-Edges-Tsonga.aspx |title=Federer Passes Tsonga Test|archivedate=26. 12. 2013|publisher=ATP World Tour|accessdate=16. 6. 2015}}</ref> Sličan je bio i polufinalni meč protiv Murrayja. Trajao je tačno četiri sata, ali je ovog puta nakon još jedne velike borbe pobijedio Murray 4–6, 7–6<sup>5</sup>, 3–6, 7–6<sup>2</sup>, 2–6.<ref>{{cite web|url=http://www.atpworldtour.com/News/Tennis/2013/01/4/Australian-Open-Friday-Federer-Murray.aspx |archiveurl= https://web.archive.org/web/20130126224047/http://www.atpworldtour.com/News/Tennis/2013/01/4/Australian-Open-Friday-Federer-Murray.aspx |title=Tennis - ATP World Tour - Murray Beats Federer To Set Up Djokovic Final Clash|archivedate=26. 1. 2013|publisher= ATP World Tour|accessdate=16. 6. 2015}}</ref><ref>{{cite web|url=http://www.australianopen.com/en_AU/news/articles/2013-01-25/201301251359112474916.html |archiveurl= https://web.archive.org/web/20130126224116/http://www.australianopen.com/en_AU/news/articles/2013-01-25/201301251359112474916.html |title=Murray makes it happen|archivedate=26. Januar1. 2013 |workpublisher=AustralianOpen.com Australian Open|accessdate=16. 6. 2015 |author= Matt Cronin}}</ref> Murray je pri 6–5 u četvrtom setu servirao za meč, ali Federer je uspio vratiti servis i izboriti ''tie-break'', koji je i dobio zahvaljujući najviše Murrayevim greškama. Ali umjesto da to slomi Murrayja desilo se obratno: Federerova igra naglo je pala u petom setu, što je Murray iskoristio i kvalitetnom igrom priveo meč kraju.
Idući nastup imao je u [[ATP Rotterdam 2013 – singl|Rotterdamu]]. Nakon lahkih pobjeda u prva dva kola protiv [[Slovenci|Slovenca]] [[Grega Žemlja|Žemlje]] i [[Holanđani]]na [[Thiemo de Bakker|De Bakkera]] u četvrtfinalu je doživio iznenađujući poraz od Benneteaua 3–6, 5–7.
