The present study aims to use systematic conservation planning to analyse and review the national protected areas (PAs) network in Jordan. The analysis included the application of three modules: the environmental risk surface (ERS), the relative biodiversity index (RBI), and the application of Marxan. The methodology was based on using Marxan to achieve solutions for three scenarios for the PAs network. Marxan was applied to the input data, which included vegetation types, distribution of threatened mammals and plants, locations of currently established PAs and other types of designations. The first two scenarios aimed to conserve 4% and 17%, respectively, of each vegetation type, and 10% and 20%, respectively, of the extent of occurrence of threatened mammals and plants. The third scenario aimed to conserve 17% of each vegetation type and 10% of the extent of occurrence of threatened plants and mammals, except for forest and the Hammada vegetation which had the target of 30% and 4%, respectively. The results of the three scenarios indicated that the boundaries of existing reserves should be extended to achieve the conservation targets. Some currently proposed (PAs), such as the Aqaba Mountains, did not appear in any of the solutions for the three scenarios indicating that the inclusion of these sites in the proposed (PAs) network should be reconsidered. All three scenarios highlighted the importance of having conservation areas between the western and eastern parts of the country. Systematic conservation planning is a structured, replicable, transparent, and defensible method for designing PA networks. It allows for finding efficient solutions building on what is currently conserved and minimizing the fragmentation and cost of the proposed solution for conservation areas.