The synaptic remodelling that occurs during activity-dependent plasticity and that is thought to underlie memory formation is incompletely understood, but complement component 1 q subcompartment-like (C1qL) proteins have been reported to be involved. Here, C1qL3 was found to be expressed in an activity-dependent manner in a subset of basolateral amygdala neurons that project to the medial prefrontal cortex (mPFC). Compared with controls, conditional C1ql3-knockout mice had fewer excitatory synapses in mPFC subregions innervated by these neurons and impaired fear memory.