A reaction processing apparatus includes: a reaction processing vessel; a first fluorescence detection device that irradiates a sample with first excitation light and detects first fluorescence produced from the sample; and a second fluorescence detection device that irradiates a sample with second excitation light and detects second fluorescence produced from the sample. The wavelength range of the first fluorescence and the wavelength range of the second excitation light overlap at least partially. The first excitation light and the second excitation light flash at a predetermined duty ratio d. The phase difference between the flashing of the first excitation light and the flashing of the second excitation light is set within a range of 2π(pm−Δpm) (rad) to 2π(pm+Δpm) (rad) or within a range of 2π[(1−pm)−Δpm] (rad) to 2π[(1−pm)+Δpm] (rad), where pm=d−d2 and Δpm=0.01*pm.