Brain-enriched guanylate kinase-associated protein (BEGAIN) interacts with postsynaptic density (PSD)-95/synapse-associated protein (SAP) 90. In immunohistochemistry and immunocytochemistry, BEGAIN was detected in nuclei and at synapses in neurons. Nuclear localization was also confirmed through subcellular fractionation. BEGAIN was localized exclusively in nuclei when expressed in epithelial cells. These findings led us to analyze the mechanism to determine the subcellular localization of BEGAIN in neurons. Green fluorescent protein (GFP)-tagged BEGAIN appeared first in nuclei and subsequently accumulated at dendrites. Approximately 75 and 90% of GFP-BEGAIN clusters were colocalized with synaptophysin and PSD-95/SAP90, respectively. GFP-protein containing only the N-terminal region also formed foci in nuclei and clusters at dendrites. The N-terminal BEGAIN was not precisely targeted to synapses, although it was partially localized at synapses, possibly through dimer formation with endogenous BEGAIN. The truncated form of PSD-95/SAP90 containing the guanylate kinase domain blocked synaptic targeting of BEGAIN but did not affect cluster formation at dendrites. NMDA receptor antagonists blocked localization of GFP-BEGAIN at synapses but did not affect recruitment to dendrites. These results suggest that BEGAIN is recruited to dendrites by the N-terminal region independently of NMDA receptor activity and that synaptic targeting of BEGAIN depends on NMDA receptor activity and may be mediated by interaction with PSD-95/SAP90.