Stager then received both his MA and PhD from Harvard, where he worked largely under the supervision of Frank Moore Cross and G. Ernest Wright, both students of William F. Albright.
The title of his thesis was Ancient Agriculture in the Judaean Desert: A Case Study of the Buqê'ah Valley in the Iron Age.
After receiving his PhD, Stager was first employed by the University of Chicago, where he taught and researched for the next fourteen years as a member of the Oriental Institute, first as an instructor (1973-4), then as an assistant (1974-6), associate (1976–1985), and finally full professor (1985-6).
In 1986, Stager returned to Harvard, where he became the inaugural holder of an endowed chair, the Dorot Professorship of the Archaeology of Israel.
Stager taught courses in Syro-Palestinian archaeology and Hebrew Bible and was an active professional member of the American Schools of Oriental Research (ASOR).