We developed a method of protein degradation in an aqueous solution containing gold nanoparticles by irradiation of a pulse laser. In the present study, lysozyme was used as an example. Lysozyme degradation proceeded most efficiently when a pH of the solution was adjusted so that it was at the isoelectric point. The scheme of the lysozyme degradation is as follows: (1) Lysozyme molecules in the solution are neutralized and adsorbed on the gold nanoparticles with its pH value adjusted at the isoelectric point, (2) nanoplasma is generated in the close vicinity of a gold nanoparticle which is excited by an intense 532-nm laser, (3) lysozyme molecules in the nanoplasma are degraded into small fragments. Lysozyme degradation does not proceed efficiently at a pH value deviated from the isoelectric point because the lysozyme molecules are dissolved uniformly so that only a small portion of the lysozyme molecules are located in the vicinity of gold nanoparticles which create the nanoplasma.