Abstract Exercise has a beneficial effect on mental health and cognitive functioning, but the exact underlying mechanisms remain largely unknown. In this review, we focus on the effect of exercise on hippocampal pattern separation, which is a key component of episodic memory. Research has associated exercise with improvements in pattern separation. We propose an integrated framework mechanistically explaining this relationship. The framework is divided into three pathways, describing the pro-neuroplastic, anti-inflammatory and hormonal effects of exercise. The pathways are heavily intertwined and may result in functional and structural changes in the hippocampus. These changes can ultimately affect pattern separation through direct and indirect connections. The proposed framework might guide future research on the effect of exercise on pattern separation in the hippocampus.