The paper proposes a systematic framework for building data-driven stochastic differential equation (SDE) models from sparse, noisy observations. Unlike traditional parametric approaches, which assume a known functional form for the drift, our goal here is to learn the entire drift function directly from data without strong structural assumptions, making it especially relevant in scientific disciplines where system dynamics are partially understood or highly complex. We cast the estimation problem as minimization of the penalized negative log-likelihood functional over a reproducing kernel Hilbert space (RKHS). In the sparse observation regime, the presence of unobserved trajectory segments makes the SDE likelihood intractable. To address this, we develop an Expectation-Maximization (EM) algorithm that employs a novel Sequential Monte Carlo (SMC) method to approximate the filtering distribution and generate Monte Carlo estimates of the E-step objective. The M-step then reduces to a penalized empirical risk minimization problem in the RKHS, whose minimizer is given by a finite linear combination of kernel functions via a generalized representer theorem. To control model complexity across EM iterations, we also develop a hybrid Bayesian variant of the algorithm that uses shrinkage priors to identify significant coefficients in the kernel expansion. We establish important theoretical convergence results for both the exact and approximate EM sequences. The resulting EM-SMC-RKHS procedure enables accurate estimation of the drift function of stochastic dynamical systems in low-data regimes and is broadly applicable across domains requiring continuous-time modeling under observational constraints. We demonstrate the effectiveness of our method through a series of numerical experiments.