A new hybrid system of molten carbonate fuel cell (MCFC) and homogenous charge compression ignition (HCCI) engine is suggested to improve the overall system efficiency and performance. In the proposed system, the catalytic burner in a standalone MCFC system is replaced with the HCCI engine. The HCCI engine is chosen over conventional spark-ignition or compression-ignition engines since it has been demonstrated to operate with highly diluted reactant mixture, which is suitable to run directly with the MCFC anode off-gas. A nonisothermal numerical model that incorporates major fuel cell losses is developed to predict the fuel cell performance. The fuel cell model assumes parallel anode and cathode flow configuration with LiNaCO3 as an electrolyte. It is integrated with an in-house HCCI engine model to investigate the hybrid system performance. At the selected design point operation around 300 kW power output, the maximum hybrid system efficiency is 21.2% (relative) higher than that of a standalone fuel cell system and, thus, achieving around 60% overall, which demonstrates the potential of the suggested hybrid system as a highly-efficient distributed power generation source in the near future.