Havill has worked with the Royal Shakespeare Company and was in The Woman in Black in London's West End in 1996. In the 2000s, his theatre roles included working with Alan Ayckbourn on his play Virtual Reality; a West End production of Jean Anouilh's Ring Around the Moon; and key roles in Director Chris Luscombe's productions of The Comedy of Errors and The Merry Wives of Windsor at Shakespeare's Globe.

Of the latter, the Guardian's Lyn Gardner wrote: "Havill's comic timing is a joy" (21 June 2008). "The real revelation is Andrew Havill as the 'cuckold' Frank Ford," wrote Quentin Letts in the Daily Mail (19 June 2008). Havill also appeared as Frank Ford in the US tour of the same play in 2010. Ben Brantley commented in The New York Times (31 Oct 2010), "As Ford... the excellent Mr. Havill is exactly as serious as he needs to be, reminding us that one of comedy’s main functions is to defuse bombs that in real life often explode and destroy.".

In 2012 and 2013 he was part of the original cast of James Graham's critically acclaimed play This House, at the National Theatre, directed by Jeremy Herrin. Other recent work has included three roles at Hampstead Theatre in the plays Farewell to the Theatre, Drawing the Line, and Wonderland.