A system for estimating for infectious disease transmission includes: a parameter receiving unit that constructs a discrete-time Markov chain model indicating a state and a state transition probability, and receives a parameter indicating status information according to the infectious disease transmission at a time point after t days have elapsed from a start of infection spread; a calculation unit that calculates the number of hidden infectious states through backward reasoning, and calculates the number of hidden infectious states through forward reasoning using the received parameter; an extraction unit that extracts an inverse scale coefficient using the calculated number of infection states and calculates a reproduction factor using the extracted inverse scale coefficient; and a prediction unit that updates infectious disease status information using the calculated reproduction factor, and predicts the number of hidden infectious persons using the updated infectious disease status information.