In order to study the optimal conditions of processing and storage for boiled and dried anchovy (Engraulis japonica) with high protein digestibility, the contents of trypsin indigestible substrate (TI) and in vitro apparent protein digestibility were determined. Peroxide value (PoV), TBA number and nonenzymatic brown pigments, that accounted for important antinutritional factors, were also measured and confirmed the relationship between those factors and formation of TI or in vitro protein apparent digestibility. The results were as follows; Samples boiled for 5 minutes showed the lower content of TI than the other samples boiled for 0.5 min. or 1 min. Hot air dried products had a lower TI content in comparison with the other dried ones such as sun dried or freeze dried products. It was revealed that the lower temperature ($8{pm}1^{circ}C$) did not affect to a great degree of forming TI and falling in vitro digestibility comparing to high temperature ($26{pm}1^{circ}C$) during storage. The lowest TI content (0.173 mg/g solid) was noted in the samples for 5 minutes and then sun drying after 56 days storage at $9{pm}1^{circ}C$. A rapid decrease of in vitro protein digestibility occurred within 0.5 min. of boiling and showed the value $85.3\%$. Freeze dried samples possessed the highest in vitro protein digestibility ($85.9\%$), when compared to sun dried or hot air dried products. Fat oxidation and nonenzymatic browning were proceeded with the various boiling times, drying methods and storing temperatures. It was noted that boiling for 5 minutes and freeze drying accelerate the fat oxidation significantly. More nonenzymatic brown pigments was developed in samples boiled for shorter time (0.5 min.) and that stored at high temperature ($26{pm}1^{circ}C$) than the other products. Therefore, fat oxidation and nonenzymatic browning assumed to be a major inhibitory reaction in enzyme digestion and those might be an important role in forming TI in boiled and dried anchovy products during processing and storage.