This study examined the effect of whole body hyperthermia on the voluntary activation of exercised and non-exercised skeletal muscle performing a series of lengthening and shortening contractions. Thirteen subjects exercised on a cycle ergometer at 60% of maximal oxygen consumption until voluntary exhaustion in ambient conditions of ~40°C and 60% relative humidity. Before and immediately following the cycle protocol, subjects performed a series of 25 continuous isokinetic shortening and lengthening maximal voluntary contractions (MVCs) of the leg extensors and forearm flexors. Voluntary activation for shortening and lengthening contractions for the forearm and leg was assessed prior to and following the 25 MVCs by superimposing a paired electrical stimulus to the femoral nerve and the biceps brachii during additional MVCs. Exercise to exhaustion increased rectal temperature to 39.35 ± 0.50°C. Voluntary activation remained unchanged following the prehyperthermia endurance set of shortening and lengthening maximal contractions in both the forearm flexors and leg extensors. Similarly, voluntary activation remained at prehyperthermic levels for the single MVCs immediately following the cycle trial. However, by the time of completion of the posthyperthermia endurance contractions, voluntary activation had declined significantly by 5.87 ± 7.56 and 8.46 ± 9.26% in the shortening and lengthening phases, respectively, for the leg extensors but not for the forearm flexors. These results indicate that the central nervous system (CNS) reduces voluntary drive to skeletal muscle performing both shortening and lengthening contractions following exercise-induced hyperthermia. The reductions in voluntary activation were only observed following a series of dynamic movements, indicating that the CNS allows for initial and brief 're-activation' of skeletal muscle following exercise-induced hyperthermia.