The brain encodes the statistical regularities of the environment in a task-specific yet flexible and generalizable format. How it does so remains poorly understood. Here, we seek to understand this by converging two parallel lines of research, one centered on striatal-dependent sensorimotor timing, and the other on hippocampal-dependent cognitive mapping. We combined functional magnetic resonance imaging (fMRI) with a visual-tracking and time-to-contact (TTC) estimation task, revealing the widespread brain network supporting sensorimotor learning in real-time. Hippocampal and caudate activity signaled the behavioral feedback within trials and the improvements in performance across trials, suggesting that both structures encode behavior-dependent information rapidly. Critically, hippocampal learning signals generalized across tested intervals, while striatal ones did not, and together they explained both the trial-wise performance and the regression-to-the-mean biases in TTC estimation. Our results suggest that a fundamental function of hippocampal-striatal interactions may be to solve a trade-off between specificity vs. generalization, enabling the flexible and domain-general expression of human timing behavior broadly.