The need for energy is increasing from year to year and has to be fulfilled by developing innovations in energy generation systems. Cogeneration is one of the matured technologies in energy generation, which has been implemented since the last decade. Cogeneration is defined as energy generation unit that simultaneously produced electricity and heat from a single primary fuel source. Currently, the implementation of this system has been spread over the world for stationary and mobile power generation in residential, industrial and transportation uses. On the other hand, fuel cells as an emerging energy conversion device are potential prime movers for this cogeneration system due to its high heat production and flexibility in its fuel usage. Even though the fuel cell-based cogeneration system has been popularly implemented in research and commercialization sectors, the review regarding this technology is still limited. Focusing on the optimal design of the fuel cell-based cogeneration system, this study attempts to provide a comprehensive review, guideline and future prospects of this technology. With an up-to-date literature list, this review study becomes an important source for researchers who are interested in developing this system for future implementation.