A photon counting device includes a plurality of pixels each including a photoelectric conversion element configured to convert input light to charge, and an amplifier configured to amplify the charge converted by the photoelectric conversion element and convert the charge to a voltage, an A/D converter configured to convert the voltages output from the amplifiers of the plurality of pixels to digital values; and a conversion unit configured to convert the digital value output from the A/D converter to the number of photons by referring to reference data, for each of the plurality of pixels, and the reference data is created based on a gain and an offset value for each of the plurality of pixels.