One of the most serious challenges facing biodiversity conservation is associated with the efficiency of protected areas for conserving biodiversity under future climate change. To address it, conservationists recommend shifting conservation planning from just focusing on protecting animal populations and their present habitat to including areas of high habitat heterogeneity. It is now well documented that range shifts of many species are occurring along altitudinal gradients. Thus, species in reserves extending over larger altitudinal gradients would have more opportunities for shifting their range toward higher altitudes. In this study, we evaluated the network of protected areas (PAs) in central Iran for their altitudinal heterogeneity. We then used a comparison index to quantify representativeness level of each altitudinal zone within the PAs. To detect if altitudinal heterogeneity may contribute in vulnerability of PAs to climate change, a climate change vulnerability assessment was performed using climate change velocity index. Our results demonstrated that the overall altitudinal heterogeneity within the PAs in central Iran is low. This was mainly attributed to the disproportionate size of the sites regarding topographic position. Among the altitudinal zones, only those at higher altitudes were well represented by the network suggesting a bias in the selection of protected sites toward higher altitudes. Altitudinal heterogeneity was found as a significant factor influencing vulnerability of the Iranian PAs to future climate change. In this regard, the sites most at risk were those distributed in east and across more topographically homogeneous landscapes. Thus, they are more urgently in need of taking actions for ameliorating the negative impacts of climate change. We suggest applying these assessments to other PAs to more completely plan for the efficiency of the Iranian PAs to future climate change.