Synapse remodeling is essential to encode experiences into neuronal circuits. Here we define a molecular interaction between neurons and microglia that drives experience-dependent synapse remodeling in the hippocampus. We find that the cytokine Interleukin-33 (IL-33) is expressed by adult hippocampal neurons in an experience-dependent manner and defines a neuronal subset primed for synaptic plasticity. Loss of neuronal IL-33 or the microglial IL-33 receptor leads to impaired spine plasticity, reduced newborn neuron integration, and diminished precision of remote fear memories. Memory precision and neuronal IL-33 are decreased in aged mice, and IL-33 gain of function mitigates age-related decreases in spine plasticity. We find that neuronal IL-33 instructs microglial engulfment of extracellular matrix (ECM), and that its loss leads to impaired ECM engulfment and a concomitant accumulation of ECM proteins in contact with dendritic spines. These data define a cellular mechanism through which microglia regulate experience-dependent synapse remodeling and promote memory consolidation.