Social behaviors, including behaviors directed toward young offspring, exhibit striking sex differences. Understanding how these sexually dimorphic behaviors are regulated at the level of circuits and transcriptomes will provide insights into neural mechanisms of sex-specific behaviors. Here, we uncover a sexually dimorphic role of the medial amygdala (MeA) in governing parental and infanticidal behaviors. Contrary to traditional views, activation of GABAergic neurons in the MeA promotes parental behavior in females, while activation of this population in males differentially promotes parental versus infanticidal behavior in an activity-level-dependent manner. Through single-cell transcriptomic analysis, we found that molecular sex differences in the MeA are specifically represented in GABAergic neurons. Collectively, these results establish crucial roles for the MeA as a key node in the neural circuitry underlying pup-directed behaviors and provide important insight into the connection between sex differences across transcriptomes, cells, and circuits in regulating sexually dimorphic behavior. Display omitted •Medial amygdala controls parenting and infanticide in a sexually dimorphic manner•GABAergic, but not glutamatergic, neurons promote parenting behavior in females•Scalable activation of GABAergic neurons in males controls parenting versus infanticide•scRNA-seq reveals molecular sex differences specifically within GABAergic neurons Sexually dimorphic displays of parenting and infanticide are differentially controlled by GABAergic neurons in the medial amygdala in an activity level-dependent manner. Single-cell transcriptomic analysis reveals cell type-specific molecular sex differences in GABAergic neurons, highlighting a connection between sexual dimorphism at levels of molecules, cells, circuits, and behavior.