Climate change is a major driver of biodiversity loss, particularly for ectothermic species such as reptiles and amphibians (hereafter herpetofauna), which are highly sensitive to environmental changes. While extensive research has evaluated the effectiveness of protected areas (PAs) in conserving biodiversity under climate change in developed and rapidly developing countries, similar studies in Africa remain scarce despite the continent’s exceptional biodiversity. This study focuses on Kenya, home to over 110 amphibians and 290 reptile species, as a model to address this conservation gap in the face of climate change. We used species distribution models (SDMs) to predict herpetofauna distributions for 2050 under three climate scenarios: SSP1-2.6, SSP2-4.5, and SSP5-8.5. Our results indicate that 20 herpetofauna species (5 amphibians and 15 reptiles) are at risk of local extinction. Furthermore, over 80% of species in both groups currently have less than 30% of their range protected within existing PAs, a trend that persists under future scenarios. We applied a systematic conservation planning approach to address this shortfall to identify priority areas for future conservation efforts. Our findings suggest that Kenya’s PA network would need to expand by approximately 16–19% of the total land area to safeguard herpetofauna both now and in the future effectively. This study underscores the urgent need to optimize Kenya’s PA network to mitigate the effects of climate change on herpetofauna. A proactive approach to conservation planning is essential to enhance species resilience and ensure their long-term survival in a rapidly changing climate.