Martin Clunes was previously married to actress Lucy Aston from 1990 to 1997. In a 2008 interview with the Mail's Weekend magazine, Clunes described that marriage as rotten. Clunes met and married his current wife, Philippa Braithwaite, in the same year as his divorce from Lucy Aston.
He proposed to Braithwaite while filming a holiday series in Hawaii. Clunes and Braithwaite have one child together, a daughter named Emily, born in 1999.