The bio-oil was largely produced by thermal pyrolysis of Jatropha-derived biomass wastes (denoted as Jatropha bio-oil) using a pilot plant with a capacity of 20 kg h-1 at Thailand Institute of Scientific and Technological Research (TISTR), Thailand. Jatropha bio-oil is an unconventional type of bio-oil, which is mostly composed of fatty acids, fatty acid methyl esters, fatty acid amides, and derivatives, and consequently, it contains large amounts of heteroatoms (oxygen ~20 wt.%, nitrogen ~ 5 wt.%, sulfur ~ 1000 ppm.). The heteroatoms, especially nitrogen, are highly poisonous to the metal or sulfide catalysts for upgrading of Jatropha bio-oil. To overcome this technical problem, we reported a stepwise strategy for hydrotreating of 100 wt.% Jatropha bio-oil over mesoporous sulfide catalysts (CoMo/γ-Al2O3 and NiMo/γ-Al2O3) to produce drop-in transport fuels, such as gasoline- and diesel-like fuels. This study is very different from our recent work on co-processing of Jatropha bio-oil (ca. 10 wt.%) with petroleum distillates to produce a hydrotreated oil as a diesel-like fuel. Jatropha bio-oil was pre-treated through a slurry-type high-pressure reactor under severe conditions, resulting in a pre-treated Jatropha bio-oil with relatively low amounts of heteroatoms (oxygen < 20 wt.%, nitrogen < 2 wt.%, sulfur < 500 ppm.). The light and middle distillates of pre-hydrotreated Jatropha bio-oil were then separated by distillation at a temperature below 240 °C, and a temperature of 240–360 °C. Deep hydrotreating of light distillates over sulfide CoMo/γ-Al2O3 catalyst was performed on a batch-type high-pressure reactor at 350 °C and 7 MPa of H2 gas for 5 h. The hydrotreated oil was a gasoline-like fuel, which contained 29.5 vol.% of n-paraffins, 14.4 vol.% of iso-paraffins, 4.5 vol.% of olefins, 21.4 vol.% of naphthene compounds and 29.6 wt.% of aromatic compounds, and little amounts of heteroatoms (nearly no oxygen and sulfur, and less than 50 ppm of nitrogen), corresponding to an octane number of 44, and it would be suitable for blending with petro-gasoline. The hydrotreating of middle distillates over sulfide NiMo/γ-Al2O3 catalyst using the same reaction condition produced a hydrotreating oil with diesel-like composition, low amounts of heteroatoms (no oxygen and less than 50 ppm of sulfur and nitrogen), and a cetane number of 60, which would be suitable for use in drop-in diesel fuel.