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Mothers who use substances during pregnancy and postpartum often have altered maternal behavior towards their infants, which can have negative consequences on infant social-emotional development. However, few studies have been conducted in the context of the neural correlates of maternal substance use and empathy towards infants, specifically the ability to recognize their feelings (cognitive empathy) and feel their emotions (affective empathy). In this study, 39 mothers who used substances (“SU”) and 42 mothers who did not (“non-SU”) underwent functional magnetic resonance imaging while viewing infant faces and hearing infant cries (Figure 1A); afterwards, they rated how much cognitive and affective empathy they felt towards those infant cues. Mothers who used substances had less affective empathy towards infant cues than mothers who did not (Figure 1B). Correspondingly, brain regions associated with affective empathy (Figure 1C) were less active in response to infant cues (Figure 1D), and activity in these brain regions statistically predicted maternal substance use status. Interestingly, cognitive empathy and activation in related brain regions were comparable between the two groups of mothers. Finally, more broadly, brain-rating correlations identified structurally and functionally dissociable brain regions associated with cognitive and affective empathy. Taken together, these results suggest specific neural and psychological processes related to maternal empathy that may contribute to differences in maternal behavior in mothers who use substances compared to mothers who do not, and speculatively suggest enhancing maternal affective empathy as a way to improve maternal behavior towards their infant.