Disorders of certain branched‐chain amino acids may be associated with the occurrence and development of non‐alcoholic fatty liver disease. Measurement of related branched‐chain amino acid levels could provide a reference for the clinical and scientific research of the non‐alcoholic fatty liver disease. An established HPLC–FLD method was used to quantify aspartic acid, glutamate, glutamine, glycine, taurine, tyrosine, 4‐amino butanoic acid, tryptophan, methionine, valine, phenylalanine, isoleucine and leucine in mouse brain tissue. Brain tissue samples mixed with internal standard (3‐aminobutyric acid) were processed, then derivatized with 2‐O‐phthaldialdehyde, and finally separated on an ODS2 column through gradient elution at a flow rate of 1.0 ml·min−1. The excitation and emission wavelengths were set at 340 and 455 nm, respectively. The mobile phase A was 100% methanol and the mobile phase B consisted of 30 mmol·L−1 sodium acetate (pH 6.8). The injection volume was 20 μl and the single run time was 45 min. Several parameters, accuracy, precision, and stability, were verified and the results showed the established method had good sensitivity and resolution for all of the 13 compounds and internal standard in mouse brain.