We present a general nonlinear Bayesian filter for high-dimensional state estimation using the theory of reproducing kernel Hilbert space (RKHS). By applying the kernel method and the representer theorem to perform linear quadratic estimation in a functional space, we derive a Bayesian recursive state estimator for a general nonlinear dynamical system in the original input space. Unlike existing nonlinear extensions of the Kalman filter where the system dynamics are assumed known, the state-space representation for the Functional Bayesian Filter (FBF) is completely learned online from measurement data in the form of an infinite impulse response (IIR) filter or recurrent network in the RKHS, with universal approximation property.