The isomeric metabolites τ- and π-methylhistidine (formerly referred to as 3- and 1-methylhistidine) are known biomarkers for muscle protein breakdown and meat protein intake, frequently used in studies involving humans and animals. In the present study, we report the development and validation of a simple HILIC-MS/MS method for individual determination of τ-MH and π-MH in a large cohort of blood plasma samples from dairy cows. Their separate determination was achieved mainly through a mass spectrometry fragment ion study, which revealed that the two isomers exhibited distinct mass spectrometric behaviors at different collision energies. Chromatographic conditions were optimised to achieve better separation, minimizing inter-channel interference to less than 1% in both directions. A simple and effective sample clean-up method facilitated low laboratory manual workload. The analytical method was validated for the determination of τ-MH and π-MH in bovine plasma within a concentration range of 80 to 1600 μg/L and provided good linearity (>0.99 for both curves) and precision (<10%). Overall, the developed method enabled the determination of the two isomers in an efficient and economic-friendly manner suitable for large cohort bovine studies (involving hundreds to thousands of samples) mainly to provide data for statistical use.