Existing physiological control fatigue models propose that there may be a regulator in the central nervous system which modulates our daily physical activity. Within limits, this regulator ensures physical activity is completed without physiological system failure through interactive communications between the peripheral systems and the central systems. The ability of the central nervous system to regulate exercise is vital to optimise sport performance when severe intensity exercise might be required for prolonged or frequent periods. Based on mathematical models, this investigation explores the complex relationship between some of the mechanisms controlling physical activity and behaviour. In order to analyse the system control mechanisms, heart rate, volume of oxygen consumption and power output were measured for a well-trained male cyclist. Using power spectrum analysis, fractal analysis and continuous wavelet transforms, we show that the system control mechanisms regulating physiological systems, have distinct complexity. Moreover, the potential central controller uses specific frequency bands simultaneously to control and communicate with the various physiological systems.We show that pacing trials are regulated by different physiological systems.