He was entered at Merchant Taylors' School in April 1802, and remained there until 1808, when he was apprenticed to Thomas Ramsden, one of the surgeons at St. Bartholomew's Hospital.
Ramsden died in 1810, and Stanley was turned over to John Abernethy to serve the remainder of his time.
Even during his apprenticeship he had rendered important services to the medical school of the hospital, for his love of morbid anatomy led him, with Abernethy's assistance and approval, to enlarge the museum so greatly that he practically created it.
Stanley was elected to the post of full surgeon in 1838, and he then rapidly became famous as a clinical teacher of great power.
He was appointed surgeon-extraordinary to the queen in 1858, and he was president of the Royal Medical and Chirurgical Society as early as 1843.