The measurement of the fractional breakdown rate (FBR) of muscle proteins during physiological non-steady state of amino acids (AAs) presents some challenges. Therefore, the goal of the present experiment was to modify the bolus stable isotope tracer injection approach to determine both fractional synthesis rate (FSR) and FBR of leg muscle protein during a physiological non-steady state of AAs. The approach uses the traditional precursor-product principle but is modified with the assumption that inward transport of AAs is proportional to their plasma concentrations. The FBR value calculated from the threonine tracer served as a reference to evaluate the validity of the FBR measurement from the phenylalanine tracer, which was under a non-steady-state condition due to the concomitant injection of unlabeled phenylalanine. Plasma phenylalanine concentration increased more than fourfold after the bolus injection, and thereafter it decreased exponentially, whereas the threonine concentration remained stable. FBR values were similar with the two tracers [0.133 ± 0.003 and 0.148 ± 0.003%/h (means ± SE) for the phenylalanine and threonine tracers, respectively, P > 0.05]. In addition, FSR values for the two tracers were similar (0.069 ± 0.002 and 0.067 ± 0.001%/h for the phenylalanine and threonine tracers, respectively, P > 0.05), indicating that the traditional FSR approach can also be used in the non-steady state. Accordingly, net balance (NB) values were similar (-0.065 ± 0.002 and -0.081 ± 0.002%/h for the phenylalanine and threonine tracers, respectively, P > 0.05). This new method of measuring muscle protein FBR during physiological non-steady state gives reliable results and allows simultaneous measurement of muscle protein FSR and thus a calculation of NB.