Abstract Efficiency is an important factor to reflect the performance of fuel cell engine (FCE). Evaluating efficiency should consider efficiency properties and common work conditions of FCE. In this paper, output power of FCE on real work conditions is analyzed according to driving cycles, and four efficiency evaluation points are obtained, as well as their weighted values. Then, a scoring function is used to convert the efficiency values of four evaluation points into scores. Multiplying scores by their weighted values and adding them together, we can get overall scores of efficiency properties. This method can evaluate the efficiency performance of FCE reasonably and objectively.