William Pitcairn established himself in London after medical studies at Leiden and Rheims and work as tutor to the Duke of Hamilton. Oxford awarded him a medical degree in 1749, and he became a fellow of the College of Physicians in 1750. That year he was elected physician to St. Bartholomew's Hospital, beginning three decades of clinical practice there. He also served as physician to Christ's Hospital.

Within the College he delivered the Gulstonian lectures in 1752, served repeatedly as censor and became president in 1775. Annually reelected, he held the presidency until 1785. At St. Bartholomew's he taught in the wards and became known for prescribing opium more freely than many contemporaries, including in cases of fever. He resigned his clinical post in 1780, subsequently became an almoner and was appointed hospital treasurer in 1784. These duties continued his work as he withdrew from private practice.

Pitcairn's other sustained pursuit was botany. At his Islington house he cultivated an garden of rare and imported plants, exchanging material through networks that linked physicians, nurserymen and university gardens. His botany helped secure election to the Royal Society in 1770. He acted as a contact for John Hope of Edinburgh in obtaining plants from London collections. He published no medical or botanical works. After leaving the College presidency, he lived between the hospital and Islington, where he died in November 1791; his garden was sold the following year.