Size-scaling metabolism is widely considered to be of significant importance in biology and ecology. Thus, allometric relationships between metabolic rate (VO2) and body mass (M), VO2 = a(i)Mb, have long been a topic of interest and speculation. It has been proposed that intraspecifically metabolic rate scales isometrically or near isometrically with body mass during the early life history in fishes, invertebrates, birds and mammals. We developed a new perspective on intraspecific size-scaling metabolism through determination of metabolic rate in the Japanese flounder, Paralichthys olivaceus, during their early life stages spanning approximately four orders of magnitude in body mass. With the increase of body mass, the Japanese flounder had four distinct negative allometric phases in which three stepwise increases in scaling constants (ai, i = 1-4), i.e. ontogenetic phase shifts in metabolism, occurred with growth during its early life stages at around 0.002, 0.01 and 0.2 g, maintaining each scaling exponent constant in each phase (b = 0.831). These shifts in metabolism during the early life stages are similar to the tiger puffer, Takifugu rubripes. Our results indicate that ontogenetic phase shifts in metabolism are key to understanding intraspecific size-scaling metabolism in fishes.