Applying facial recognition technology to support academic information systems to enhance the security of information systems that support online learning and consultation is significant for information technology and engineering pedagogy. Therefore, this research aims to (1) synthesize the relevant components and technologies to develop the prototype of a two-factor authentication system using artificial intelligence technology, (2) develop the prototype of a two-factor authentication system to increase the efficiency and capacity of identity verification, and (3) evaluate the acceptance of the prototype of a two-factor authentication system. The research tools included a questionnaire on components of developing the academic information system, a two-factor authentication system prototype, and a quality assessment form for the information system’s acceptance. The results revealed that the accepted prototype consisted of four modules: An authentication module, a member module, an information module, and a management module, with the overall quality assessment results at a strongly acceptable level (x = 4.44, S. D. = 0.55).