Ben Whishaw grew up in Bedfordshire, with his twin brother, James, and was a member of the Bancroft Players Youth Theatre at Hitchin's Queen Mother Theatre. He attended Samuel Whitbread Community College in Clifton, Bedfordshire. During his time with the group, he first rose to prominence during collaborations with their offshoot theatre company, Big Spirit. He was involved in many productions - perhaps most notably, If This Is A Man (also performed as The Drowned & The Saved). This was a piece devised by the company based on the book of the same name by Primo Levi, a survivor of a Nazi World War II prisoner of war camp. This harrowing and moving book was adapted into a physical theatre piece by the group and taken to the 1995 Edinburgh Festival where it garnered five-star reviews and great critical acclaim. Whishaw played the character of Levi in this and subsequent productions of the show.

As the lead in Trevor Nunn's 2004 young-cast production of Hamlet at the Old Vic, he received highly favourable reviews. The role was shared with Al Weaver in an unusual arrangement that saw Whishaw playing all nights except for Mondays and matinées. Nunn is reported to have made this arrangement due to the youth of the two actors playing the lead, to relieve some of the pressure on each. It was Whishaw, however, who featured most prominently in the marketing materials and in the majority of reviews.

Whishaw's film and TV credits include Layer Cake and Chris Morris's 2005 sitcom Nathan Barley, in which he played a character called Pingu. He was named 'Most Promising Newcomer' at the 2001 British Independent Film Awards (for My Brother Tom) and, in 2005, nominated as best actor in four award ceremonies for his Hamlet. He also played Keith Richards in the Brian Jones biopic Stoned. In the spring of 2005, Whishaw received lots of press for his turn as a drug dealer in Philip Ridley's post-apocalyptic fringe play Mercury Fur.

In Perfume, Whishaw plays Jean-Baptiste Grenouille, a perfume maker whose craft turns deadly. The film was released in Germany in September 2006 and in the U.S. in December 2006. In the same year Whishaw worked on Pawel Pawlikowski's abandoned The Restraint of Beasts.

Whishaw appears in 2007's I'm Not There as one of the Bob Dylan reincarnations and in 2008 in Criminal Justice, a Tiger Aspect series for the BBC.

He appears in the forthcoming films The International, a new adaptation of Brideshead Revisited, and Bright Star. In 2008 he will star in “...some trace of her”, an adaptation of The Idiot at the National Theatre.