Based on previous work indicating different neural substrates, two aspects of energetic state, arousal and activation, have been conceptualised separately in our laboratory. Arousal has been defined as the energetic state at any particular time, and task-related activation as the task-related change in state from resting baseline to the task situation. Both are reflected in electrodermal activity and measured by skin conductance level. Our previous studies in this area have indicated that physiological responses to stimuli in a task are dependent on the arousal level at the time of stimulus presentation, rather than the task-related activation. In contrast, performance on the task is dependent on the task-related activation, rather than the current arousal level. That is, different aspects of the individuals state determine physiological and behavioural responses. Those studies had examined between-subjects differences in arousal and activation. The present study investigated the relevance of this separation in an across-subjects examination of fluctuations in arousal and activation, and their effects on physiological and behavioural responses, during a continuous performance task. It was found that the magnitude of the phasic Orienting Reflex to the targets during the task was dependent mainly on arousal, rather than task-related relative activation. Reaction time improved with increasing relative activation, but not with arousal. These findings support our earlier conclusions relating to the usefulness of arousal and activation as distinguishable features of the energetics of physiological and behavioural functions.