Backfire of hydrogen‐fuelled internal combustion engines limits the hydrogen fuel applications and drops the power output. Opposed rotary piston (ORP) engines are characterized by high power density, smooth operations, and few moving parts. However, the intake structures of ORP engines tend to deliver high possibility of backfire under hydrogen utilization conditions due to more residual exhaust. This paper proposed an effective approach of eliminating backfire for a hydrogen fuelled ORP engine, and it did not generate any penalty of power output theoretically. The effectiveness of this method was demonstrated using a 3D numerical simulation method. The results indicated that the average in‐cylinder temperature started to increase at the start of the intake process if without any backfire control strategies; however, it decreased continuously if backfire control was applied. The mass flow rates of the intake fluid were at a low level without backfire control, but it increased sharply if backfire control was adopted. Backfire in this investigation was caused by the pre‐ignition of mixture in cylinders. The temperature in intake pipes reached up to 1000 K over backfire scenarios, and heat of reaction was higher than 3 W. Hydrogen mass fractions at the bottom of intake pipes were low at the start of intake process due to the backfire; meantime, slight backflow also happened in the intake process due to the pre‐ignition of cylinders mixture. The fluid velocity was higher than 100 m/s at the beginning of intake process if backfire was controlled.