Rationale The psychoactive substance, caffeine may improve cognitive performance, but its direct impact on learning and memory remains ill-defined. Conflicting reports suggest that caffeine may impair as well as enhance Pavlovian fear conditioning in animals, and its effect may vary across different phases of learning. Objectives To dissect the effect of a motor-stimulant dose of caffeine (30 mg/kg i.p.) on acquisition, retrieval or consolidation of conditioned fear in C57BL/6 mice. Methods Fear conditioning was evaluated in a conditioned freezing paradigm comprising 3 tone-shock pairings and a two-way active avoidance paradigm lasting two consecutive days with 80 conditioning trials per test session. Results Conditioning to both the discrete tone conditioned stimulus (CS) and the context was markedly impaired by caffeine. The deficits were similarly evident when caffeine was administered prior to acquisition or retrieval (48 and 72 h after conditioning); and the most severe impairment was seen in animals given caffeine before acquisition and before retrieval. A comparable deficit was observed in the conditioned active avoidance test. By contrast, caffeine administered immediately following acquisition neither affected the expression of tone freezing nor context freezing. Conclusions The present study challenges the previous report that caffeine primarily disrupts hippocampus-dependent conditioning to the context. At the relevant dose range, acute caffeine likely exerts more widespread impacts beyond the hippocampus, including amygdala and striatum that are anatomically connected to the hippocampus; and together they support the acquisition and retention of fear memories to discrete stimuli as well as diffused contextual cues.