Glutamatergic synapse maturation involves as a critical step the replacement of developmentally-expressed N-methyl-D-aspartate receptors (NMDARs) with mature forms which differ in subunit composition, electrophysiological properties, and propensity to elicit synaptic plasticity. However, the mechanisms underlying the removal and replacement of synaptic NMDARs are poorly understood. Here we show that NMDARs containing the non-conventional NR3A subunit undergo rapid endocytosis from the dendritic surface in cultured rat hippocampal neurons. Endocytic removal is regulated by the intracellular adaptor PACSIN1/syndapin1, which directly and selectively binds the carboxy-terminal domain of NR3A through its NPF motifs and assembles a complex of proteins including dynamin and clathrin. Further, interaction with PACSIN1 directs the sorting of NR3A-containing NMDAR subtypes between degradative/recycling pathways. Endocytosis of NR3A by PACSIN1 is activity-dependent, and disruption of PACSIN1 function causes NR3A accumulation at synaptic sites. Together, these findings reveal a novel activity-dependent mechanism involved in the synaptic regulation of NMDARs during development, and identify a brain-specific endocytic adaptor that confers spatiotemporal and subunit specificity to NMDAR endocytosis. Funding provided by NARSAD, NIH, Marie Curie IRG, and Hereditary Disease Foundation.