The main idea of the investigation was to define testing parameters with the lowest influence of internal and external diffusion on catalytic activity in hydrodesulfurization of dibenzothiophene. Traditional experimental methods were used to determine the conditions for the influence of internal and external diffusion. Simultaneous change of a linear feedstock rate and a catalyst loading at constant weight hour space velocity were used to determine the process temperature (240–260 °C) at which the impact of external diffusion is minimal. Catalytic tests, including the variation of the catalyst fraction size, were carried out to define the conditions with the lowest influence of internal diffusion. It was found that when the catalyst with the fraction size of 0.1–0.25 mm was used, the fluctuation of sulfur conversion was the smallest. Besides, to validate experimental results, the calculations were performed with mass balance equations and expressions used for HDS modeling. The resulting data and catalytic experiments demonstrated that the lowest influence of internal and external diffusion is achieved at a temperature process less than 260 °C and a catalyst fraction of 0.1–0.25 mm.