He was the first Director of the Whitechapel Art Gallery from 1901 to 1911, and became Keeper at the Tate Gallery in 1911. In 1917 he changed his title from "Keeper" to "Director". Sir John Rothenstein described Aitken as "an ordinary man: his intelligence was relatively pedestrian, his powers of self-expression scarcely adequate". However, Rothenstein considered that the job "brought out qualities that made him a great director: clarity and firmness of purpose".
When the art critic of The Daily Telegraph wrote an article claiming that the sculptures of Jacob Epstein had been universally condemned by critics, Epstein wrote instancing the support of Aitken among other leading names in the art world. In 1909 Aitken co-founded the Modern Art Association, which in 1910 was renamed the Contemporary Art Society.
Following his retirement from the position of Director in 1930, he was appointed a Companion of the Order of the Bath (CB) in the 1931 King's Birthday Honours. He died on 9 August 1936.