Background Citrulline malate (CM), especially when used in conjunction with physical exercise, has demonstrated potential as a non-pharmacological adjunct in the management of hypertension. Nevertheless, its impact on nocturnal blood pressure dipping remains unexplored. Objective Evaluate the impact of a single dose of CM on nocturnal blood pressure dipping after exercise in hypertensive individuals. Methods In a double-blind, placebo-controlled, parallel-group clinical trial, twenty hypertensive adults (55 ± 16 years) were randomly assigned to either a CM (6 g) or placebo (6 g of corn starch) group (PLA). Resting blood pressure was measured after a 20-min period of comfortable seating in a calm environment. Both groups underwent 40 min of treadmill running/walking at an intensity of 60–70% of their reserve heart rate, 120 min after ingesting the substances. Ambulatory blood pressure monitoring was employed to measure blood pressure over 24 h. Results No significant differences in systolic blood pressure values were observed between the CM and PLA groups at rest, during wakefulness, sleep, or over a 24-h period. However, CM exhibited a significant reduction in diastolic blood pressure in several metrics: delta 24 h (-14 mmHg vs −6 mmHg, p = 0.047), delta wakefulness (-12 mmHg vs −4 mmHg, p = 0.024), percent delta 24 h (-16% vs −6%, p = 0.024), and percent delta wakefulness (-14% vs −4%, p = 0.013). No significant differences were found between CM and PLA in terms of systolic and diastolic nocturnal absolute reductions (-13 mmHg vs −12 mmHg, p = 0.808, and −13 mmHg vs −8 mmHg, p = 0.273, respectively) or nocturnal percentage decrease (-9.9% vs −9.4%, p = 0.844, and −15.3% vs −11.7%, p = 0.399, respectively). Conclusions The study found no significant changes in the post-exercise nocturnal blood pressure dip following a single dose of CM supplementation. However, a notable reduction in diastolic blood pressure was observed during the waking period and over the average 24-h monitoring period. Clinical trial registry number and website ClinicalTrials.gov platform (NCT03378596).