He enrolled at St Bartholomew's Hospital as a medical student in 1879, but in the following year transferred to Christ's College, Cambridge to read natural sciences, specialising in zoology.

[1] Shipley particularly specialised in the study of parasitic worms, publishing nearly fifty papers on them and leading to his election as a Fellow of the Royal Society in 1904.

He stayed at Cambridge after graduation, being appointed university demonstrator in comparative anatomy in 1886, lecturer in the advanced morphology of the Invertebrata in 1894, and reader in zoology in 1908.

Other popular publications included: Pearls and Parasites[2] (1908), "J": a Memoir of John Willis Clark (1913), The Minor Horrors of War (1915; about parasites), More Minor Horrors (1916), Studies in Insect Life (1917), The Voyage of a Vice-Chancellor (1919), Life (1923), Cambridge Cameos and Islands: West Indian and Aegean (1924), and Hunting under the Microscope (1928).

In recognition of this work and other wartime services (including making the Christ's College Master's Lodge available as a convalescent home for wounded officers), Shipley was appointed Knight Grand Cross of the Order of the British Empire (GBE) in the 1920 civilian war honours.