Habitat fragmentation has major negative impacts on wildlife populations and the connectivity could reduce these negative impacts. This study was conducted to assess habitat suitability and structural connectivity of the Persian leopard along the Iran-Iraq border (i.e., the Zagros Mountains) and compare the situation of identified core habitats and connectivity with existing conservation areas (CAs). An ensemble modeling approach resulting from five models was used to predict habitat suitability. To identify core habitats and corridors along the Iran-Iraq border, factorial least-cost path analyses were applied. The results revealed that topographic roughness, distance to conservation areas, annual precipitation, vegetation/cropland density and distance to rivers were the most influential variables for predicting the occurrence of the Persian leopard in the study area. By an estimated dispersal distance of 82 km (suggested by previous studies), three core habitats were identified (two cores in Iran and one core in Iraq). The largest cores were located in the south and the center of the study area, which had the highest connectivity priorities. The connectivity from these cores was maintained to the core within the Iraqi side. Only about one-fifth of detected core habitats and relative corridors were protected by CAs in the study area. Detected core habitats and connectivity areas in this study could be an appropriate road map to accomplish the CAs network along the Iran-Iraq border regarding Persian leopard conservation. Establishing transboundary CAs, particularly in the core habitat located in the center of the study area, is strongly recommended to conserve existing large carnivores, including the Persian leopard.