This dataset comprises 4D-DIA quantitative proteomics data from primary rat brain microvascular endothelial cells (BMECs) subjected to Oxygen-Glucose Deprivation/Reoxygenation (OGD/R) injury. The aim of the study was to investigate the protective mechanism of the novel protein AABR40, encoded by the lncRNA AABR07033564.1. Comparative proteomic analysis was performed between BMECs overexpressing AABR40 and control vectors following OGD/R insult. Bioinformatic analysis of the proteomic data identified BNIP3 as a key downstream effector, which was subsequently validated to mediate mitophagy. The raw data supports the finding that AABR40 inhibits pyroptosis by activating BNIP3-dependent mitophagy, providing a potential therapeutic target for ischemic brain injury.