This chapter synthesizes the foundational role of circadian rhythms (CRs) as ubiquitous endogenous biological timing systems that are primarily responsible for synchronizing organisms to the 24-hour environmental cycle. Their detailed architecture involves a hierarchical organization in which the central pacemaker, the suprachiasmatic nucleus (SCN), governs tissue-specific peripheral clocks through coordination by the molecular machinery of the transcriptional–translational feedback loop (TTFL). Circadian rhythms are critically important in rehabilitation sciences, as they regulate essential physiological processes such as physical performance, muscle strength, and the rhythmic secretion of key hormones, including growth hormone and cortisol. Importantly, sustained circadian misalignment, referred to as chronodisruption, is strongly associated with the pathophysiology of chronic musculoskeletal pain and the development of heightened central sensitization. This dysregulation often manifests clinically as abnormal vascular rhythms, such as non-dipper blood pressure patterns. Chronotherapy offers a strategic framework to correct this temporal dissonance through the timed application of potent environmental synchronizers, or Zeitgebers. These include structured exercise timing (chronexercise), controlled light exposure, and rigorous sleep hygiene practices. This review highlights the scientific imperative for physiotherapists to integrate principles of circadian biology into clinical practice to optimize patient recovery trajectories and maximize physiological responsiveness.