A series of NiMo/alumina catalysts modified with phosphorus was prepared and evaluated in a trickle-bed high-pressure flow micro-reactor. The kinetics of deep hydrodesulfurization (HDS) of dibenzothiophene (DBT) and 4,6-dimethyldibenzothiophene (DMDBT) was investigated based on conversion and products distribution data. The estimated parameters obtained were statistically significant, suggesting an accurate representation of the system. Phosphorus addition led to a two-fold increase in the formation of direct desulfurization over hydrogenation products for the HDS of DBT. On the other hand, the HDS of DMDBT increased mainly due to an increase in the hydrogenation route, leading to high yields of hydrogenated products. The observed phenomena were described well by the estimated parameters and may be related to an increase in metal dispersion, formation of more active sites and enhancement in Bronsted acidity in the catalyst upon phosphorus addition.