We propose a novel nonparametric approach for linking covariates to Continuous Time Markov Chains (CTMCs) using the mathematical framework of Reproducing Kernel Hilbert Spaces (RKHS). CTMCs provide a robust framework for modeling transitions across clinical or behavioral states, but traditional multistate models often rely on linear relationships. In contrast, we use a generalized Representer Theorem to enable tractable inference in functional space. For the Frequentist version, we apply normed square penalties, while for the Bayesian version, we explore sparsity inducing spike and slab priors. Due to the computational challenges posed by high-dimensional spaces, we successfully adapt the Expectation Maximization Variable Selection (EMVS) algorithm to efficiently identify the posterior mode. We demonstrate the effectiveness of our method through extensive simulation studies and an application to follicular cell lymphoma data. Our performance metrics include the normalized difference between estimated and true nonlinear transition functions, as well as the difference in the probability of getting absorbed in one the final states, capturing the ability of our approach to predict long-term behaviors.