The present invention relates to a public transportation payment method and system using a beacon. More particularly, the public transportation payment system comprises: a beacon, installed in an entrance and an exit of a transportation means, which recognizes a user terminal approaching an established Near Field Communication area and sends a public transportation payment authentication key to the recognized user terminal; a public transportation terminal, installed in the transportation means, which collects identification information of the recognized user terminal via the beacon and assigns the public transportation payment authentication key on the basis of the collected information; a public transportation management server which is connected to the public transportation terminal installed in the transportation means via a network and performs an approval process for the payment approval requested from a public transportation-use application installed on the user terminal using the transportation means; and a user terminal which, if the public transportation payment authentication key is sent via the beacon installed in the transportation means, requests the approval process from the public transportation management server via the public transportation-use application.