A bio-hydrogenated diesel (BHD) becomes more attractive fuel due to its use without engine modification and high heating value. This work aims to evaluate the possibility of using low-grade, potential resources, i.e., waste cooking oil and palm fatty acid distillate (PFAD), which is a byproduct from palm oil refinery, to produce BHD. A systematic methodology through a thermodynamic insight is applied to designing the BHD production process. Two alternatives in waste cooking oil processing are considered; the first one (A1) involves the esterification process coupled with a hydrotreating process and the second one (A2) concerns about the direct hydrotreating process. The production of BHD from PFAD (B) is based on the hydrotreating process. Modeling of the BHD processes is performed using Aspen Plus simulator. All the proposed processes are designed with the BHD specification of 99.5% purity. Regarding the economic analysis, the use of PFAD for the BHD production offers more benefit than that of waste cooking oil in terms of net present value, return on investment and payback year.