During brain development, excess synapses are pruned (i.e., removed), in part by microglial phagocytosis, and dysregulated synaptic pruning can lead to behavioral deficits. The P2Y receptor (P2YR) is known to regulate microglial phagocytosis of neurons, and to regulate microglial phagocytosis of synapses in cell culture and during aging. However, currently it is unknown whether P2YR regulates synaptic pruning during development. Here, we show that P2YR KO mice of both sexes had strongly reduced microglial internalization of synaptic material, measured as Vglut1 within CD68-staining lysosomes of microglia at postnatal day 30 (P30), suggesting reduced microglial phagocytosis of synapses. Consistent with this, we found an increased density of synapses in the somatosensory cortex and the CA3 region and dentate gyrus of the hippocampus at P30. We also show that adult P2YR KO mice have impaired short- and long-term spatial memory and impaired short- and long-term recognition memory compared with WT mice, as measured by novel location recognition, novel object recognition, and Y-maze memory tests. Overall, this indicates that P2YR regulates microglial phagocytosis of synapses during development, and this contributes to memory capacity. The P2Y receptor (P2YR) is activated by uridine diphosphate released by neurons, inducing microglial phagocytosis of such neurons or synapses. We tested whether P2YR regulates developmental synaptic pruning in mice and found that P2YR KO mice have reduced synaptic material within microglial lysosomes, and increased synaptic density in the brains of postnatal day 30 mice, consistent with reduced synaptic pruning during development. We also found that adult P2YR KO mice had reduced memory, consistent with persistent deficits in brain function, resulting from impaired synaptic pruning. Overall, the results suggest that P2YR mediates microglial phagocytosis of synapses during development, and the absence of this results in memory deficits in the adult.