We consider the problem of learning Stochastic Differential Equations of the form $dX_t = f(X_t)dt+σ(X_t)dW_t $ from one sample trajectory. This problem is more challenging than learning deterministic dynamical systems because one sample trajectory only provides indirect information on the unknown functions $f$, $σ$, and stochastic process $dW_t$ representing the drift, the diffusion, and the stochastic forcing terms, respectively. We propose a method that combines Computational Graph Completion and data adapted kernels learned via a new variant of cross validation. Our approach can be decomposed as follows: (1) Represent the time-increment map $X_t \rightarrow X_{t+dt}$ as a Computational Graph in which $f$, $σ$ and $dW_t$ appear as unknown functions and random variables. (2) Complete the graph (approximate unknown functions and random variables) via Maximum a Posteriori Estimation (given the data) with Gaussian Process (GP) priors on the unknown functions. (3) Learn the covariance functions (kernels) of the GP priors from data with randomized cross-validation. Numerical experiments illustrate the efficacy, robustness, and scope of our method.