A secondary authentication system and computer-implemented method for obtaining real-time cardholder authentication of a payment transaction associated with a cardholder's payment card includes a memory device for storing data and a processor communicatively coupled to the memory device. The processor is programmed to receive a payment authorization request message including a primary account number corresponding to a payment account of the cardholder for funding the payment transaction. In addition, the processor is programmed to determine whether the payment account requires secondary authentication by the cardholder for the payment transaction, and if, based on the determination, the payment account requires secondary authentication of the payment transaction, place the payment transaction on hold. Furthermore, the processor is programed to identify a mobile device associated with the payment account of the cardholder, transmit an authentication request message to the identified mobile device, and receive, from the mobile device, an authentication response message.