Significance Microglia are the brain’s resident immune cells, surveying the brain with motile processes, which can remove pathogens but also prune unnecessary junctions between the neurons (synapses). A potassium channel, THIK-1, in the microglial membrane allows efflux of potassium from these cells and thereby regulates their membrane voltage as well as their process motility and release of inflammatory mediators. Here, using THIK-1–blocking drugs and THIK-1–deficient mice, we demonstrate that THIK-1 controls removal of synaptic material by microglia, which reduces the number of functional synapses in the developing brain.