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In recent years, scientific investigations on the effectiveness of Protected Areas (PM) in conserving biodiversity and sustaining ecosystem functions under the impact of climate change have increasingly received more attention from researchers and park managers. In this study, we used a combination of species distribution modelling (SDM) and spatial hierarchical systematic conservation planning technique to delineate and prioritize areas for endemic plant species conservation under current and future (2050s, 2070s) climate conditions in Sikkim Himalaya. Data on endemic plant species occurrence were sourced from our already published studies and their potential suitable habitats under current and future climates were modelled using Maximum Entropy (MaxEnt) SDM. The MaxEnt habitat suitability projections of species were used in Zonation software to identify priority conservation areas in Sikkim Himalaya. We found that the existing PA network in the region was inadequate in conserving the endemic plant diversity either in the current or future climate scenarios. Based on our results, we propose addition of 896 square kilometres (sq km) to the existing PA network in the study area to ensure meaningful conservation goals. Additionally, we propose creation of 3 new PM (Yumsedong, Lachen and Chungthang) and the need for expanding the boundaries of existing PM (Maenam, Fambong Lho and Barsey) in the study area. Our analyses show that to mitigate the effects of ensuing climate change, a single large PA with wide geographic and elevational extents instead of several smaller PM would be a more prudent strategy for conserving the plant diversity in the Himalaya.