Estimating heterogeneous treatment effects (HTE) is crucial for identifying the variation of treatment effects across individuals or subgroups. Most existing methods estimate HTE by removing the confounding bias from imbalanced treatment assignments. However, these methods may produce unreliable estimates of treatment effects and potentially allocate suboptimal treatment arms for underrepresented populations. To improve the estimation accuracy of HTE for underrepresented populations, we propose a novel Stable CounterFactual Regression (StableCFR) to smooth the population distribution and upsample the underrepresented subpopulations, while balancing confounders between treatment and control groups. Specifically, StableCFR upsamples the underrepresented data using uniform sampling, where each disjoint subpopulation is weighted proportional to the Lebesgue measure of its support. Moreover, StableCFR balances covariates by using an epsilon-greedy matching approach. Empirical results on both synthetic and real-world datasets demonstrate the superior performance of our StableCFR on estimating HTE for underrepresented populations.