Aitchison became an Associate of the Royal Academy in 1978, and was elected as one of the 80 Members of the Royal Academy (or Royal Academicians) in 1988. He resigned from the Academy in 1997 in protest over the display of Marcus Harvey's work Myra, but rejoined in 1998. In 1996 he was commissioned to paint a mural of Calvary — a landscape illuminated by a mystical light — for the Gothic Revivalist Truro Cathedral in Cornwall. In 1997, he was commissioned to paint Calvary for Liverpool Cathedral, and he created a design for a Christmas stamp for the Royal Mail in 1999. Further sacred works by Aitchison are held the chapel of King's College, Cambridge. Retrospectives of his work were held at the Serpentine Gallery in 1981, at Harewood House near Leeds in 1994, and at the Gallery of Modern Art in Glasgow in 1996. Other shows were held at the Museum of Modern Art, Powys in 2001 and at the Royal Academy in London in 2003. He won the Royal Academy's Korn Ferry International Award in 1989 and in 1991, won the first £30,000 Jerwood Painting Prize, sponsored by The Sunday Telegraph in 1994, and won the Nordstern Art Prize in 2000. He was made a Commander of the Order of the British Empire (CBE) in 1999. Several of his works are held in the collection of the Tate Gallery. He designed the Tate Gallery's Christmas tree and Christmas card in 1992. Birmingham Museums & Art Gallery and the National Galleries of Scotland also own works.