Two experiments were conducted with flounder to examine phytase pretreatment or dietary phytase supplement for improving phosphorus (P) utilization of soybean meal (SBM) or soy protein concentrate (SPC). In experiment I, three SBM based‐diets, SBM (basal), phytase‐supplemented SBM (supplement), and phytase‐pretreated SBM (pretreatment), were fed to flounder, and digestibilities of P, gross energy (GE) and crude protein (CP) were measured by an indirect method. In experiment II, three SPC based‐diets including P‐supplemented mineral mixture (control), P‐free mineral mixture (unsupplemented), or P‐free mineral mixture supplemented with phytase (supplement) were fed to flounder for 50 days, and growth, whole‐body P composition, and plasma mineral concentration were determined. In experiment I, a significantly higher absorption of P was found in fish fed the pretreatment or supplement diet compared to the fish fed the basal diet. In experiment II, the growth of fish fed the supplement diet was comparable to that of the control and better than that of fish fed the unsupplemented diet. Whole‐body P retention and plasma P concentrations of supplement‐fed fish were significantly higher than those of fish fed the unsupplemented diet. These results suggest that phytase supplementation to the SBM‐ or SPC‐based diets improves phytase‐bound P availability for Japanese flounder.