A system and method for securely distributing quantum keys in a network are disclosed. The method includes receiving request for generating pair of quantum keys between source quantum node and target quantum node. Further, the method includes generating first pair of quantum keys based on the request. The method includes transmitting the first pair of quantum keys to the intermediate quantum node using a first quantum link. The method further includes generating intermediate pair of quantum key based on events detected at the intermediate quantum node. The method further includes interleaving the intermediate pair of quantum key with the first pair of quantum keys. Also, the method includes generating a second pair of quantum keys comprising interleaved intermediate pair of quantum key and first pair of quantum keys. Further, the method includes encoding and transmitting the second pair of quantum keys to target quantum node using second quantum link.