We consider the variable selection problem for two-sample tests, aiming to select the most informative variables to determine whether two collections of samples follow the same distribution. To address this, we propose a novel framework based on the kernel maximum mean discrepancy (MMD). Our approach seeks a subset of variables with a pre-specified size that maximizes the variance-regularized kernel MMD statistic. We focus on three commonly used types of kernels: linear, quadratic, and Gaussian. From a computational perspective, we derive mixed-integer programming formulations and propose exact and approximation algorithms with performance guarantees to solve these formulations. From a statistical viewpoint, we derive the rate of testing power of our framework under appropriate conditions. These results show that the sample size requirements for the three kernels depend crucially on the number of selected variables, rather than the data dimension. Experimental results on synthetic and real datasets demonstrate the superior performance of our method, compared to other variable selection frameworks, particularly in high-dimensional settings.