Born in Bury St. Edmunds, Suffolk, Maloney's first television appearance was as Peter Barkworth's teenage son in the 1979 drama series, Telford's Change.

After several dry years in his career, Maloney went on to star in many films and television series, as well as developing a stage career and became a familiar face after playing a major role in Kenneth Branagh's 1989 film adaptation of Henry V. In the early 1990s, he starred on television in Mr Wakefield's Crusade, and on film as Mark in Truly, Madly, Deeply, and in 1994 he took the lead in the BBC adaptation of Love on a Branch Line. He appeared in both the 1990 and 1996 film versions of Hamlet, as Rosencrantz and Laertes respectively, and in several other Shakespeare screen adaptations. In addition to his TV appearances, he starred as Jason Fields in the film American Reel in 1999. 2002 saw him play Brian Albumen, personal aide to Rik Mayall's Adonis Cnut character in the Gran and Marks penned TV sitcom Believe Nothing. In 2003, he appeared as the Belgian Prosper Profond in The Forsyte Saga. He also played Cassius in the 2005 miniseries Empire, John Major in 2009's Margaret and Prime Minister Sir Robert Peel in the 2009 film The Young Victoria.

In 2010, he appeared in long-running drama Casualty as consultant Howard Fairfax, and in series 4 of the political satire series The Thick of It, he played Matthew Hodge, part of the Goolding Inquiry. In 2013, he portrayed Sir Henry Stafford, third husband of Lady Margaret Beaufort, in the BBC TV series The White Queen. In 2016, he appeared in the ITV/Netflix series Paranoid.

He has also lent his voice to various video-game characters. The Lost Soul in the 2013 video-game Castlevania: Lords of Shadow - Mirror of Fate, Avallac'h in the 2015 video-game The Witcher 3: Wild Hunt, and Doloran in the 2018 video-game Ni no Kuni II: Revenant Kingdom.