Linton was born into a family of Quaker restaurant entrepreneurs in Philadelphia in 1893 and entered Swarthmore College in 1911. He was an indifferent student and resisted his father's pressures to prepare himself for the life of a professional. He grew interested in archaeology after participating in a field school in the southwest and took a year off of his studies to participate in another archaeological excavation at Quiriguá in Guatemala. Having found a strong focus he graduated Phi Beta Kappa in 1915.