The article presents the research results on performance, thermodynamic parameters, and toxic exhaust emissions from the combustion in a compression-ignition engine fueled optionally by the hydrotreated vegetable oil (HVO) or the rapeseed methyl ester (RME), both with hydrogen addition. Furthermore, regular diesel fuel was used to obtain the reference data for making comparisons between HVO, RME, and diesel fuel. Hydrogen was injected into the intake manifold of a compression-ignition (CI) engine. Typically, diesel fuel combustion in a CI engine initiates through its self-ignition, usually simultaneously occurring at many points across the engine cylinder. Hydrogen, as a very chemically reactive substance, can promote pre-ignition reactions and accelerate flame kernel formation, shortening the ignition lag. This is crucial for the smooth running of the compression-ignition engine. Hydrogen was added at amounts not exceeding 7% by volume (35% energy content) referred to air sucked into the engine cylinder. As observed, a slightly positive trend in NOx vs. hydrogen addition was observed. It was also found that hydrogen added in small amounts does not form the so-called knock originating from hydrogen rapid combustion, regardless of the diesel knock.