In this paper, we study how the Koopman operator framework can be combined with kernel methods to effectively control nonlinear dynamical systems. While kernel methods have typically large computational requirements, we show how random subspaces (Nystr\"om approximation) can be used to achieve huge computational savings while preserving accuracy. Our main technical contribution is deriving theoretical guarantees on the effect of the Nystr\"om approximation. More precisely, we study the linear quadratic regulator problem, showing that both the approximated Riccati operator and the regulator objective, for the associated solution of the optimal control problem, converge at the rate $m^{-1/2}$, where $m$ is the random subspace size. Theoretical findings are complemented by numerical experiments corroborating our results.