Red bigeye fish with less than 15 cm length are categorized as low-value fish. The aim of this study was to determine the protein profiles of red bigeye flesh. Red bigeye flesh was analyzed for proximate analysis, LC-QTOF-MS analysis and Fourier transform infrared FTIR. It was found that red bigeye flesh contained 17.21% crude protein, 1.82% crude fat, 1.34% ash content and 3.42% carbohydrate. LC-MS/MS analysis revealed 83 unique proteins, including troponin 33, myosin 23, actin 19, tropomyosin 6, and parvalbumin 2. Regulatory proteins gave the largest portion of 51%, followed by enzymes at 28.92%, and unreviewed proteins at 20.48%. Red bigeye flesh proteins exhibited higher levels of post-translational modifications (PTMs) mainly oxidation and mutation. FTIR spectra analysis of red bigeye flesh protein exhibiting symmetrical bending stretches within amide regions A, B, I, II, III, and VII. This study shows that red bigeye flesh proteins is a promising source of functional food.