Background and Objectives: Controlled breathing can influence autonomic regulation and haemodynamics; however, the role of its timing relative to exercise remains unclear. Materials and Methods: Fourteen healthy, physically active men (mean age 21.8 ± 0.7 years; body mass index within the normal range) participated in this randomised crossover study. Each session consisted of five 5 min cycling bouts at 50% of heart-rate reserve, interspersed with 3 min passive recovery periods. The three conditions were: control (no structured breathing), 30 s hyperventilation (approximately 30 breaths·min⁻¹) performed before each bout, and the same hyperventilation performed after each bout. Resting heart rate variability spectra (low-frequency [LF], high-frequency [HF]) were assessed pre- and post-session; arterial blood pressure was measured stage-wise; quadriceps muscle oxygen saturation (StO₂) was monitored using near-infrared spectroscopy; and a discriminant co-integration index (Dsk) was calculated to integrate multisystem responses. Results: Compared with baseline, LF power increased and HF power decreased after exercise in the control and post-exercise hyperventilation conditions (p < 0.05), whereas pre-exercise hyperventilation attenuated these shifts. Post-exercise hyperventilation blunted the rise in systolic blood pressure and reduced diastolic blood pressure compared with control (p < 0.05). Both breathing interventions accelerated StO₂ recovery, with higher early recovery StO₂ following pre-exercise hyperventilation and sustained advantages after post-exercise hyperventilation (moderate-to-extensive effects). Dsk values were consistently highest after exercise, indicating stronger and more coherent multisystem coupling. Conclusions: In this acute crossover study of healthy young men, hyperventilation performed before or after exercise induced distinct short-term cardiovascular and muscular responses, reflecting respiratory-driven modulation of haemodynamic and autonomic processes. The timing of hyperventilation influenced these responses, suggesting that deliberate hyperventilation may acutely modify exercise-related regulatory mechanisms.