The influence of hydrogen on the catalytic deoxygenation of fatty acids was investigated in the semibatch reactor over a mesoporous 5 wt % Pd/C (Sibunit) catalyst. Transformations of a model fatty acid (lauric acid) and reaction intermediates (lauric aldehyde and lauryl alcohol) were performed under inert and hydrogen rich atmosphere. Analysis of the liquid and gas phases of the reaction mixture revealed that different reactions occurred depending on hydrogen content in the reaction atmosphere. A higher yield of hydrocarbons (59 mol %) was obtained in the fatty acid deoxygenation under hydrogen pressure compared to an experiment under argon where the yield of hydrocarbons reached 39 mol % after 300 min of the reaction. Different product distributions, intermediates and reaction pathways depending on hydrogen content in the reaction atmosphere, are discussed.