Objective N-methyl-D-aspartate (NMDA) receptor subunit 2B (NR2B) and its phosphorylation are involved in cerebral ischemia/hypoxic neural injury. Hypoxic preconditioning (HPC) can serve as an endogenous protective intervention to protect the brain from ischemic/hypoxic injury. This study intended to explore the effect of HPC on NR2B and the phosphorylation of its two tyrosine sites (1252 and 1336) in hippocampal cells through in vivo and in vitro experiments and thus determine the role of NR2B in HPC neuroprotection. Methods 6~8 weeks-old male SPF-grade ICR mice and the mouse hippocampal neuron cell line HT22 were repeatedly exposed to hypoxia to replicate HPC animal and cell models. Western blot and immunofluorescence were applied to detect the levels of NR2B and the phosphorylation levels of its tyrosine 1336 (pY1336NR2B) and 1252 (pY1252NR2B) residues in the hippocampus of mice and HT22 cells. The distributions of NR2B, pY1336NR2B, and pY1252NR2B in the synaptic site (TxP) and extrasynaptic site (TxS) were analyzed by Western blot. The levels of cleaved caspase-3 and α-spectrin, which indicate cell apoptosis, were also detected. Results HPC downregulated the levels of NR2B and pY1336NR2B in the mouse hippocampus and HT22 cells. Changes in NR2B and pY1336NR2B levels in the TxS of the mouse hippocampus were similar to those in hippocampus and HT22 cells, whereas changes in the TxP showed the opposite trend. Conclusions Downregulation of NR2B and pY1336NR2B may be involved in HPC-induced neuroprotection, and their localization at synapses and extrasynapses may play different roles in neuroprotection.