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Abstract This paper is concerned with solving, from the learning-based decomposition control viewpoint, the problem of output tracking with nonperiodic tracking–transition switching. Such a nontraditional tracking problem occurs in applications where sessions for tracking a given desired trajectory are alternated with those for transiting the output with given boundary conditions. It is challenging to achieve precision tracking while maintaining smooth tracking–transition switching, as postswitching oscillations can be induced due to the mismatch of the boundary states at the switching instants, and the tracking performance can be limited by the nonminimum-phase (NMP) zeros of the system and effected by factors such as input constraints and external disturbances. Although recently an approach by combining the system-inversion with optimization techniques has been proposed to tackle these challenges, modeling of the system dynamics and complicated online computation are needed, and the controller obtained can be sensitive to model uncertainties. In this work, a learning-based decomposition control technique is developed to overcome these limitations. A dictionary of input–output bases is constructed offline a priori via data-driven iterative learning first. The input–output bases are used online to decompose the desired output in the tracking sessions and design an optimal desired transition trajectory with minimal transition time under input-amplitude constraint. Finally, the control input is synthesized based on the superpositioning principle and further optimized online to account for system variations and external disturbance. The proposed approach is illustrated through a nanopositioning control experiment on a piezoelectric actuator.