To quicken the process for high global warming potential (GWP) working fluid replacement for organic Rankine cycle (ORC) systems, a thermo-economic evaluation of low GWP fluid R1233zd(E) as an R245fa alternative has been performed in comparison with other natural fluids n-Pentane, Isopentane, and Isobutane for geothermal applications. The heat source water mass flow rate remains constant and 5K pinch point is set for both evaporator side and condenser side. All working fluids have a close net thermal efficiency within 2%. Increasing the heat source from 120 °C to 160 °C gives a more than 20% efficiency rise. The low critical temperature of Isobutane limits its application for 160 °C heat source. R1233zd(E) displays a close mass flow rate (within 2%) from R245fa and others exhibit more than 40% flow rate reduction. The component level performance has also been investigated in this study. All alternatives exhibit a lower evaporator side (evaporator and preheater) heat transfer area than baseline R245fa, and a slightly higher condenser side (condenser and desuperheater) heat transfer area. For turbine performance, R245fa displays the highest volume flow ratio, indicating a significant change of the rotor blade height should be made between the inlet and outlet point for the expansion process. R1233zd(E) displays ~10% increase for turbine size parameter from baseline, n-Pentane shows ~22% rise, Isopentane exhibits ~11% rise, while Isobutane presents 32% decrease, respectively. In general, R1233zd(E) only exhibits ~2.3% higher specific investment cost than R245fa, while n-Pentane and Isopentane exhibit more than 15% cost rise. Thus, from the thermo-economic scale with an extended application range, R1233zd(E) exhibits a better overall performance index when compared with other R245fa alternatives and can be serviced as promising candidate to replace R245fa.