Non-enzymatic reactions between proteins and methylglyoxal (MG) result in the formation of advanced glycation end products (AGEs). These AGEs play a vital role in the development of diabetic complications by stimulating oxidative stress and acting upon their receptor RAGE (Receptor for Advanced Glycation End products). This study examined the effect of aqueous methanol extract of Bombax ceiba L. calyxes (BCCE) on MG induced protein glycation and oxidative stress, followed by the identification of phytometabolites present in the calyxes using gas chromatography-mass spectrometry (GC-MS). The study revealed that priming of bovine serum albumin protein with the BCCE inhibited MG induced AGE formation in vitro and restrained AGE-induced RAGE up-regulation in HEK-293 cells. The BCCE significantly (p < 0.001) reduced the MG induced increase in reactive oxygen species (ROS), NADPH oxidase (NOX), and mitochondrial dysfunction. Improvements in the levels of antioxidant enzymes such as Mn and Cu/Zn-superoxide dismutase and glutathione reductase were also observed in HEK-293 cells. Furthermore, the decrease in primary cellular defense against AGEs, the glyoxalase 1 (Glo-1) activity, due to MG treatment was restored in BCCE treated cells. GC-MS analysis revealed the presence of antioxidant and antiglycation compounds such as myo-ionisitol, scopoletin, d-sedoheptulose, succinic acid, and xylitol in B. ceiba calyxes. The observed beneficial effect in our study might be attributed to the presence of these compounds in B. Ceiba calyxes. This is the first report presenting the antioxidant and antiglycation activities of B. ceiba calyxes and GC-MS analysis of active phytometabolites. These observations show that B. ceiba calyxes may become a potent and promising functional food to manage/control the development of diabetic complications.