[3] Flanagan died on 31 August 2009, aged 68, from motor neurone disease in Santa Eulalia del Río, Ibiza, Spain.

[4] He was the subject of a South Bank Show in 1983 directed by Don Featherstone and a biographical film by Peter Bach, The Man Who Sculpted Hares: Barry Flanagan, A Life.

[5][6] Castings of Flanagan's Thinker on a Rock are installed at Washington University in St. Louis,[7][8] the John and Mary Pappajohn Sculpture Park in Des Moines, Iowa,[9] Utrecht,[10] O’Connell Street in Dublin,[3] the Philbrook Museum of Art, in Tulsa, OK,[11] and the National Gallery of Art Sculpture Garden (Washington, D.C.)[12][13][14] Flanagan's hare statue, Large Left-Handed Drummer, was on display in Union Square, Manhattan from 18 February to 24 June 2007.

This exhibition contained many examples of his less well known pieces using materials such as cloth and rope, as well as some early bronze hare sculptures for which he gained renown.

At an exhibition held by Sotheby's at Chatsworth House, Derbyshire, in September–October 2012, fifteen of Flanagan's works were shown in a parkland setting.