A protected area network is effective only when it adequately covers the samples of important ecological, ecoregion, elevation and physiographical regions including critically endangered biota of a region. This study used geographic information system and conducted a chronological analysis for ecological, ecoregion, elevation and physiographical representativeness of protected area system of Nepal since 1970s to present. A Comparison Index was used for the analysis. Current system of protected area system was analyzed for degree of fragmentation by using index of fragmentation. Though Nepal has set aside sizable areas i.e. 23.33% total area for protected area network, the analysis identified many gaps in current network.