The present invention provides a means of economically, quickly and efficiently designing a physiologically active peptide to a target protein. Specifically, the present invention provides a method of designing a physiologically active peptide characterized in that, to design a physiologically active peptide capable of binding to a target site comprising a consecutive or non-consecutive amino acid sequence in a target protein, a computerized processing is carried out for extracting a preferable amino acid sequence by calculating intermolecular energy etc.; an apparatus therefor; a program for executing the above-described processing by a computer; and a computer-readable recording medium containing the program.