There is a great demand for novel disinfection technologies to inactivate various pathogenic viruses and bacteria. In this situation, ultraviolet (UVC) disinfection technologies seem to be promising because biocontaminated air and surfaces are the major media for disease transmission. However, UVC is strongly absorbed by human cells and protein components; therefore, there are concerns about damaging plasma components and causing dermatitis and skin cancer. To avoid these concerns, in this study, we demonstrate that the efficient inactivation of bacteria is achieved by visible pulsed light irradiation. The principle of inactivation is based on transient photothermal heating. First, we provide experimental confirmation that extremely high temperatures above 1000 K can be achieved by pulsed laser irradiation. Evidence of this high temperature is directly confirmed by melting gold nanoparticles (GNPs). Inorganic GNPs are used because of their well-established thermophysical properties. Second, we show inactivation behaviour by pulsed laser irradiation. This inactivation behaviour cannot be explained by a simple optical absorption effect. We experimentally and theoretically clarify this inactivation mechanism based on both optical absorption and scattering effects. We find that scattering and absorption play an important role in inactivation because the input irradiation is inherently scattered by the bacteria; therefore, the dose that bacteria feel is reduced. This scattering effect can be clearly shown by a technique that combines stained Escherichia coli and site selective irradiation obtained by a wavelength tunable pulsed laser. By measuring Live/Dead fluorescence microscopy images, we show that the inactivation attained by the transient photothermal heating is possible to instantaneously and selectively kill microorganisms such as Escherichia coli bacteria. Thus, this method is promising for the site selective inactivation of various pathogenic viruses and bacteria in a safe and simple manner.