Increased volatility in global rubber prices has led to declining Malaysian rubber production and smallholder income. Identifying rubber clones that can produce a consistently high yield in various environments is one of the potential measures to alleviate the impact of price fluctuations and improve smallholder livelihoods. In this study, we assessed rubber yields and yield stability of 37 rubber tree clones at two major production regions in Malaysia: Kota Tinggi (Southern region) and Sungai Buloh (Central region). In addition, we assessed relationships between climate data with rubber yields. Rubber yield and stability differed widely by clone, but showed relatively consistent trends across regions. Clones RRIM 2007, PB 260, and RRIM 2012 were high yielding in both regions and had high stability. Conversely, clone RRII 308 had the lowest mean yield across both regions and low stability. Mean annual yields showed a negative relationship with rising minimum temperatures, declining by ~3 g per tapping per tree (g t−1 t−1) per 1 °C rise in minimum temperature. Our findings highlight clones capable of achieving stable high yields. This information may be useful for breeders and agronomists in identifying germplasm and traits for further development. Further, this information can be used to assist clone recommendations to smallholders in these regions to mitigate the dual impacts of climate change and market volatility.