For the promotion of the development and utilization of biofuels, it is important to secure a supply of biomass feedstock from which biofuels will be derived. In the present study, analysis of the energy balance and of CO2 emissions for the management of Jatropha plantations was carried out, assuming that the Jatropha plantations would be developed in the Philippines where the climatic and farming conditions are suitable for the plant growth. The evaluation was conducted for the reclamation of farmland, Jatropha cultivation, and oil mill processing. The value of the energy profit ratio (EPR), defined as the ratio of energy input to energy output for the entire system, was determined to be 7.3, which could be increased by reducing chemical fertilization. However, because biodiesel fuel conversion consumes a substantial amount of energy, production of unprocessed oil may be preferable. CO2 emissions for the production of Jatropha oil were estimated at 20 g CO2/MJ, with a low negative environmental impact.