There are considerably fewer requirements for the quality of hydrogen combusted in an engine than its quality for fuel cells. Therefore, the analysis was carried out on the combustion of hydrogen–helium mixtures in an engine with a two-stage combustion system (TJI—Turbulent Jet Ignition). A single-cylinder research engine with a passive and active prechamber was used. A hydrogen–helium mixture was supplied to the main chamber in proportions of 100:0, 90:10, 80:20, 30:70, and 60:40 volume fractions. The prechamber was fueled only with pure hydrogen. Combustion was carried out in the lean charge range (λ = 1.5–3) and at a constant value of the Center of Combustion (CoC = 8–10 deg aTDC). It was found that the helium concentration in the mixture affected the changes in combustion pressure, heat release rate and the amount of heat release. It was observed that increasing the proportion of helium in the mixture by 10% also reduces the IMEP by approximately 10% and reduces the rate of heat release by approximately 20%. In addition, helium influences knock combustion. Limits of MAPO = 1 bar mean assumed that knock combustion occurs in the main chamber at values of λ < 1.9. Increasing the excess air ratio results in a gradual reduction in the temperature of the exhaust gas, which has a very rapid effect on changes in the concentration of nitrogen oxides. Studies carried out on the helium addition in hydrogen fuel indicate that it is possible to use such blends with a partial deterioration of the thermodynamic properties of the two-stage combustion process.