MacGillivray was educated at Marischal College in the University of Aberdeen. His father, William, was appointed a professor there in 1841, a teacher of natural history. During his time as a student, Paul wrote and published a catalogue, entitled A Catalogue of the Flowering Plants and Ferns growing in the neighbourhood of Aberdeen, with the help and support of his father. However, when MacGillivray's father died in September 1852, he lost interest in the studies of science, and instead chose to practise medicine, in London. Later that year, MacGillivray decided to migrate to Melbourne, Australia.
There he continued his medicine practice, and began worked at Williamstown, where he joined a local, voluntary fire brigade, where he served as the brigade's medical officer. Later, between the years of 1862 and 1873, MacGillivray acted as a surgeon in the hospital of Bendigo, where he organised a private medical practice. While MacGillivray's deepest interest remained natural history, he showed great talent and potential in medicine, and he produced numerous papers and essays in relation to surgery and surgical matters. His work was indeed so prolific and insightful that he was elected president of the Medical Society of Victoria. Paul MacGillivray also became known as one of the most prominent and notable Australian naturalists of the time. Following his talent as a naturalist, MacGillivray was selected as a member of the Philosophical Institute of Victoria. Among other naturalistic accomplishments, MacGillivray wrote several papers in relation to nature, some illustrated, as well as undertaking several projects of research. Additionally, at a later stage in his life, MacGillivray formed strong relations and a membership with the Field Naturalists' Club of Victoria.
Death
Paul MacGillivray died on 9 July 1895 at his house in Bendigo. It was at this time that he close to completing a large monograph for the Royal Society of Victoria. He was survived by Elizabeth, née Shields, his wife, five daughters and a son. His collections, papers, findings and library were brought forth to the National Museum of Victoria by the government shortly after his death.