Microglial synaptic engulfment has been histologically confirmed; however, direct real-time evidence is lacking on whether and how microglia engulf synapses in living neurons. To answer the questions, we develop a novel in vitro system of neuron-glia cocultures in which microglia maintain their natural morphology with highly ramified processes. Using the system, we examined how synaptic engulfment is controlled when the “eat-me” signal, complement C1q, ubiquitously exists in the brain parenchyma as in pathological conditions. Live-imaging analysis revealed that microglia engulf en passant synapses without snipping off axons. C1q significantly increased synaptic engulfment when microglial surveillance was induced by elevated neuronal activity. These results suggest that neuronal activity triggers microglial encounter with “eat-me” signals. To confirm our findings in vivo, we used a mouse model of febrile seizures in which microglia preferentially engulf inhibitory synapses, even though C1q are deposited on both excitatory and inhibitory synapses. We determined that sustained activity of inhibitory neurons after seizures induces the inhibitory synapse-specific engulfment. Thus, our findings suggest that complement-dependent synaptic engulfment is triggered and spatially controlled by neuronal activity.