MacGillivray was born in Aberdeen and brought up on the island of Harris. He returned to Aberdeen where he studied medicine at King’s College. In 1823 he became assistant to the Professor of Natural History at Edinburgh University. He was Curator of the museum of the Royal Society of Surgeons in Edinburgh from 1831, and Professor of Natural History at Marischal College, Aberdeen from 1841. He died in Aberdeen and was buried in Edinburgh’s New Calton cemetery.
He was a friend of John James Audubon, and wrote large part of Audubon’s Ornithological Biographies from 1830-1839. His own works include A Biography of Alexander von Humboldt (1833), Lives of eminent zoologists from Aristotle to Linnaeus (1834), A Systematic Arrangement of British Plants (1835), A History of British Quadrupeds (1838), A manual of botany, comprising vegetable anatomy and physiology (1840), A History of the Molluscous Animals of Aberdeen, Banff and Kincardine (1843), A Manual of British Ornithology (1840 – 1842), and A History of British Birds, indigenous and migratory, in five volumes (1837-1852). His Natural History of Deeside and Braemar (1855) was published posthumously.
Audubon named MacGillivray's Warbler for him.