Kinnear's performances in Phyllida Lloyd's production of Mary Stuart and Trevor Nunn's Hamlet, in which he played Laertes, met with acclaim. He also achieved recognition as the outrageous Sir Fopling Flutter in The Man of Mode at the National Theatre, winning a Laurence Olivier Award and Ian Charleson Award. Other notable theatre work includes the lead in Thomas Middleton's The Revenger's Tragedy, the role of Pyotr in Maxim Gorky's Philistines and the role of Mitia in a stage adaptation of the Nikita Mikhalkov film Burnt by the Sun, all for the National Theatre. In 2010, he played Angelo in Measure for Measure at the Almeida Theatre. Later in 2010 he played the title role in Hamlet at the National Theatre. The two portrayals won him the best actor award in the Evening Standard drama awards for 2010. Kinnear appeared in The Last of the Haussmans by Stephen Beresford at the National Theatre during the summer of 2012. The production was broadcast to cinemas around the world on 11 October 2012 through the National Theatre Live programme. He starred as Iago opposite Adrian Lester in the title role of Othello in 2013 at the National Theatre throughout the summer of 2013. Both actors won the Best Actor award in the Evening Standard Theatre Awards for their roles; the award is normally given to only one actor, but the judges were unable to choose between the two men. From September 2013, the Bush Theatre in London staged Kinnear's debut play The Herd, directed by Howard Davies. The play ran at the Steppenwolf Theatre in Chicago beginning 2 April 2015. In October 2017 he appeared in the title role of Young Marx, the premiere production at the Bridge Theatre. He returned to the Olivier Theatre at the National Theatre to star as the title role in Macbeth with Anne-Marie Duff from February 2018.
For The Threepenny Opera at the Olivier Theatre from May to October 2016, Kinnear found his "dormant" singing voice for the role of Macheath. In February 2017 he made his directing debut with The Winter's Tale, a new opera written by Ryan Wigglesworth and based on Shakespeare's play, for English National Opera.
He currently portrays Bill Tanner in the Daniel Craig era James Bondfilm series after taking over from Michael Kitchen. He is the fourth person to play the character. He has appeared in Quantum of Solace, Skyfall and Spectre. As well as the films, Kinnear also lends his voice and likeness to the Bond video games; GoldenEye 007, and 007 Legends. In 2014, he played the fictional character, Detective Nock, in The Imitation Game based loosely on the biography Alan Turing:The Enigma by Andrew Hodges. In January 2017 he portrayed Ellmann in the Netflix film iBoy. He played Henry Hunt in Mike Leigh's 2018 film Peterloo.
Further to his theatre work he received particularly positive reviews for his sympathetic portrayal of Denis Thatcher in The Long Walk to Finchley, a BBC dramatisation of the early years of Margaret Thatcher's political career, which also starred Andrea Riseborough and Samuel West. He also starred alongside Lucy Punch and Toby Stephens in the BBC Two series Vexed. Broadcast on 19 October 2010, he was the co-lead in the BBC4 TV drama, The First Men in the Moon written by and co-starring Mark Gatiss. In 2011, he provided narration during the BBC Proms production of 'Henry V – suite' arranged by Muir Mathieson during their Film Music Prom. He appeared in the lead role of Prime Minister Michael Callow in "The National Anthem", the first episode of the anthology series Black Mirror. In July 2012, Kinnear appeared as Bolingbroke in Richard II, a BBC Two adaptation of the play of the same name, with Ben Whishaw as King Richard and Patrick Stewart as John of Gaunt. From 2013 onwards, he has starred in the BBC series Count Arthur Strong as Michael. He has also appeared in the Channel 4 drama Southcliffe. In December 2013 he appeared as British peer and suspected murderer Lord Lucan in the two-part ITV series Lucan. He also appeared as Frankenstein's monster in the Showtime television series Penny Dreadful, which premiered 11 May 2014. In 2017 he appeared in the British miniseries Guerrilla as a Chief Inspector in the Special Branches. In 2017 he starred as Robert Lessing in the BBC Two comedy series Quacks, which ridicules the early days of medicine in England. In 2018 he appeared in the first episode of the fourth series of the BBC One comedy series Inside No. 9, Zanzibar, which being a Shakespearean parody, was written in mainly rhyming couplets, with Rory Kinnear playing identical twins and long-lost sons. In 2019, Kinnear played Craig Oliver in the Channel 4 television film ., and the desperate financial advisor Stephen Lyons in the futuristic series Years and Years.
In 2010, he played Flugkapitän Jürgen Rahl in the BBC Radio drama Slipstream as a disaffected German pilot who joins a mission to steal an alien spacecraft harboured by the Nazis.
Kinnear is engaged to actress Pandora Colin. The couple have a son, Riley, born in 2010 and a daughter, Hope, born in 2014. He announced that his sister Karina Kinnear died from the coronavirus at the age of 48 in May 2020.