Disclosed is an apparatus for counting single photons including an edge combiner configured to detect an edge of each of applied clocks using a plurality of Phase-Locked Loops (PLL) to generate a combined signal; a sampling unit configured to sample all events occurring in each SPAD of a single photon detection diode (SPAD) array using an OR tree and an XOR tree; and a calculation unit configured to count the sampled events based on the combined signal to count single photons.