Previous studies have detected activity-independent fish thermoregulation or conservation mechanisms by applying a mathematical model to body temperature data collected with electronic tags. This model is inadequate, due to its inability to separate quantitatively the effects of physiological thermoregulation from those of physical thermal inertia (the low thermal conductance of the body). In this paper, we have developed an alternative mathematical model that separates these effects. We have then applied it to published electronic tagging data from a large, free-swimming blue shark, Prinoca glauca, to demonstrate physiological thermoregulation. Resultant estimated body-temperature curves indicate that the fish could adjust its whole-body heat-transfer coefficient by changes in arterial blood flow over a range of one order of magnitude. To look at the physical effect on thermoregulation, body temperature for a smaller hypothetical fish was calculated. The estimated temperature was significantly lower than the actual value, indicating that an ectothermic fish like the blue shark cannot achieve physiological thermoregulation without assistance from thermal inertia. In addition, the blue shark returns to cooler depths without recovering its body temperature to the normal surface-temperature level, indicating that this behavior contributes to maximization of the rate of body-temperature recovery. Furthermore, the model indicated that the time for body-temperature recovery is irrelevant to the initial body temperature. Thus, the model made it possible to quantify thermophysiological manipulation. In addition, it was also useful in the comparison of thermoregulatory mechanisms between fishes of different sizes or species.