Acute stress is associated with a shift from goal-directed to habitual behavior. This stress-induced preference for habitual behavior has been suggested as a potential mechanism by which binge eating disorder (BED) patients succumb to eating large amounts of high-caloric foods in an uncontrolled manner (i.e., binge episodes). While in healthy subjects the balance between goal-directed and habitual behavior is subserved by the anterior cingulate cortex (ACC), insular cortex, orbitofrontal cortex (OFC), anterior caudate nucleus, and posterior putamen, the brain mechanism that underlies this (possibly amplified) stress-induced behavioral shift in BED patients is currently unknown. In the current study, 76 participants (38 BED, 38 healthy controls (HCs)) learned six stimulus-response-outcome associations in a well-established instrumental learning task. Subsequently, three outcomes were selectively devalued, after which participants underwent either a stress induction procedure (Maastricht Acute Stress Test; MAST) or a no-stress control procedure. Next, the balance between goal-directed and habitual behavior was assessed during functional magnetic resonance imaging. Findings show that the balance between goal-directed and habitual behavior was associated with activity in the ACC, insula, and OFC in no-stress HCs. Although stress and BED did not modulate the balance between goal-directed and habitual behavior, BED participants displayed a smaller difference in putamen activation between trials probing goal-directed and habitual behavior compared with HCs when using a ROI approach. We conclude that putamen activity differences between BED and HC could reflect changes in monitoring of response accuracy or reward value, albeit perhaps not sufficiently to induce a measurable shift from goal-directed to habitual behavior. Future research could clarify potential boundary conditions of stress-induced shifts in instrumental behavior in BED patients.