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).
In 2009, a Festschrift for Stager was published under the title Exploring the Longue Durée: Essays in Honor of Lawrence E. Stager (Ed. J. David Schloen; Winona Lake, Ind.: Eisenbrauns).
Stager's most important archaeological work was conducted through the Leon Levy Expedition to Ascalon, of which he became the director in 1985. This expedition is one of the largest and lengthiest projects in Israel. The results of the dig have been published in the Harvard Semitic Museum and Eisenbrauns' Ashkelon, a series of ten volumes, the third of which was published in 2011.
Prior to his monumental undertakings at Ashkelon, Stager worked on digs at Carthage, Idalion, Gezer, and Tell el-Hesi.
Stager generally adhered to the traditional scholarly dating of the "United Monarchy" of King David and Solomon.
J. D. Schloen, ed. Exploring the Longue Durée: Essays in Honor of Lawrence E. Stager (Winona Lake, Ind.: Eisenbrauns, 2009).