On 7th March, 1754, Craik resumed his military career, accepting a commission as a surgeon in Colonel Joshua Fry's Virginia Provincial Regiment. While with this force, he became good friends with George Washington, at that time a lieutenant colonel in the regiment. Craik saw a great deal of action in various battles of the French and Indian War. He fought at the Battle of the Great Meadows and participated in the surrender of Fort Necessity, then accompanied General Edward Braddock on the latter's unsuccessful attempt to recapture the region in 1755, treating Braddock's ultimately fatal wounds.
Craik then served under Washington in actions in Virginia and Maryland, during various engagements with Indians.
With the outbreak of hostilities during the American Revolution, Craik once more rejoined the army. He served as an army surgeon, ultimately advancing to the second-highest post in army medicine. Craik warned Washington about the plots of the Conway Cabal and treated the wounds of General Hugh Mercer at the Battle of Princeton and Gilbert du Motier, Marquis de La Fayette, at the Battle of Brandywine. Mercer died of his wounds, but La Fayette was more fortunate.
Washington summoned Craik out of private practice in 1798 in connection with the Quasi-War against France, installing him as Physician General of the Army on June 19th of that year. After the conclusion of hostilities, Craik mustered out on June 15th, 1800.
As Washington's personal physician, Craik was one of three doctors to attend him during his final illness on December 14th, 1799.
Craik died in Alexandria in 1814. He is buried in the graveyard of the Old Presbyterian Meeting House there.