A pattern recognition system, pattern recognition method, and pattern recognition program capable of increasing the accuracy in computing the false acceptance probability and capable of ensuring a stable security strength are provided. Pattern recognition systems 10 and 10a comprise a first probability computation unit 32, and a second probability computation unit 33 coupled to the first probability computation unit 32. The first probability computation unit 32 computes a first probability PFCR based on the number n of corresponding characteristic points cs1 to csn and cf1 to cfn indicating points corresponding between characteristic points s1 to sns in a first pattern and characteristic points f1 to fnf in a second pattern. The first probability PFCR indicates the probability of existence of a third pattern that has a greater number of corresponding characteristic points to the first pattern than the number n of the corresponding characteristic points. The second probability computation unit 33 refers to the first probability PFCR to compute a false acceptance probability PFAR indicating the probability of falsely determining that the first pattern and the second pattern correspond to each other.