Crude jatropha oil (JO) was modified to form jatropha oil-based polyol (JOL) via two steps in a chemical reaction known as epoxidation and hydroxylation. JOL was then reacted with isocyanates to produce JO-based polyurethane resin. In this study, two types of isocyanates, 2,4-toluene diisocyanate (2,4-TDI) and isophorone diisocyanate (IPDI) were introduced to produce JPUA-TDI and JPUA-IPDI respectively. 2,4-TDI is categorised as an aromatic isocyanate whilst IPDI is known as a cycloaliphatic isocyanate. Both JPUA-TDI and JPUA-IPDI were then end-capped by the acrylate functional group of 2-hydroxyethyl methacrylate (HEMA). The effects of that isocyanate structure were investigated for their physico, chemical and thermal properties. The changes of the functional groups during each synthesis step were monitored by FTIR analysis. The appearance of urethane peaks was observed at 1532 cm−1, 1718 cm−1 and 3369 cm−1 while acrylate peaks were detected at 815 cm−1 and 1663 cm−1 indicating that JPUA was successfully synthesised. It was found that the molar mass of JPUA-TDI was doubled compared to JPUA-IPDI. Each resin showed a similar degradation pattern analysed by thermal gravimetric analysis (TGA). For the mechanical properties, the JPUA-IPDI-based coating formulation exhibited a higher hardness value but poor adhesion compared to the JPUA-TDI-based coating formulation. Both types of jatropha-based polyurethane acrylate may potentially be used in an ultraviolet (UV) curing system specifically for clear coat surface applications to replace dependency on petroleum-based chemicals.