We developed a technology (capturing activated neuronal ensembles CANE) to label, manipulate, and transsynaptically trace neural circuits that are transiently activated in behavioral contexts with high efficiency and temporal precision. CANE consists of a knockin mouse and engineered viruses designed to specifically infect activated neurons. Using CANE, we selectively labeled neurons that were activated by either fearful or aggressive social encounters in a hypothalamic subnucleus previously known as a locus for aggression, and discovered that social-fear and aggression neurons are intermixed but largely distinct. Optogenetic stimulation of CANE-captured social-fear neurons (SFNs) is sufficient to evoke fear-like behaviors in normal social contexts, whereas silencing SFNs resulted in reduced social avoidance. CANE-based mapping of axonal projections and presynaptic inputs to SFNs further revealed a highly distributed and recurrent neural network. CANE is a broadly applicable technology for dissecting causality and connectivity of spatially intermingled but functionally distinct ensembles. •CANE is a new technology for capturing activated (Fos+) neuronal ensembles•CANE tags Fos+ neurons with high specificity, temporal precision, and efficiency•Hypothalamic neurons eliciting social-fear behaviors are identified using CANE•CANE-based mapping reveals a highly distributed and recurrent social-fear circuit Sakurai et al. developed a new technology (CANE) to capture and manipulate recently activated (Fos+) neurons in the mouse brain. CANE is applied to delineate the causal functions and connectivity of hypothalamic neurons activated by a social-fear experience.