A fluorescence detection method allows fluorescence intensity detection from a fluorescently-labeled biological sample with high accuracy in shorter time, even when a fluorescence intensity from a microchip itself acting as background. A fluorescence intensity from an equivalent microchip, which is equivalent to a microchip with the fluorescently-labeled biological sample, is detected for a period from the start of application of excitation light until the intensity sufficiently attenuates, and a temporal change of the intensity is stored. The light is applied to the microchip and the sample is fed before the fluorescence intensity from the microchip sufficiently attenuates to detect the fluorescence intensity for a period from the start of application of the light to a point after the sample is fed. Values of the temporal change are subtracted from the intensity detected from the microchip with the sample to detect an intensity of fluorescence emitted from the sample.