Pacing during exercise performance is well-established; however, little is known about the neural responses associated with changes in power output and the effect of exercise end-point knowledge. Therefore, the aim of this study was to examine the effect of deception of cycling distance on pacing, cerebral oxy- (O2Hb) and deoxy-haemoglobin concentrations, and alpha (α) wave activity. Ten well-trained male cyclists (23.7 ± 6.6 years) completed three cycling time trials (TT) on a stationary air-braked cycle ergometer and were informed the study was to examine the reliability of 3 × 30-km TT. Participants unknowingly completed three distances (24, 30, and 36 km) in a randomised order. Performance (power output; PO), physiological (heart rate; HR), perceptual (rating of perceived exertion; RPE), and neurological (O2Hb, HHb, and α activity) measures were recorded throughout each TT. Data were converted to a percentage relative to the total distance covered. At 100% completion, HR and PO were lower during the 36 km compared to the 30 km trial (P ≤ 0.01). Compared to the 24 km trial, α waves were reduced at 100% (effect size; ES = 1.01), while O2Hb was greater at 70% of completion in the 36 km trial (ES = 1.39). RPE was also higher for 36 km compared to 30-km trial at 80% and the 24-km trial at 10% and 40–100% of completion (P ≤ 0.02). We conclude that the increase in O2Hb and RPE during the 36-km trial, while a reduction in HR and PO is present, may indicate that the pre-frontal cortex may influence the regulation of exercise performance when deceived of the duration end-point by increasing perception of effort to reduce premature onset of physiological strain.