His sister, Susan Shippen, was married to Samuel Blair, the second Chaplain of the United States House of Representatives.

[3][4] He studied with Reverend Samuel Finley at West Nottingham Academy and then attended the College of New Jersey (now Princeton University), graduating in 1754.

He became one of the first professors (of anatomy, surgery, and midwifery) of America's first medical school (the College of Philadelphia, now the University of Pennsylvania), which he co-founded in 1765 with Dr. John Morgan.

[2] Like his father, William Shippen Jr. was elected to the revived American Philosophical Society in 1767, where he served as Curator from 1771 to 1772, and as Secretary from 1772 to 1773.

He was subsequently court martialed for misappropriating supplies intended for recovering soldiers and underreporting deaths, but was acquitted on a technicality.