Emotion is characterized by dimensions of affective valence and arousal, either or both of which may be altered by sleep loss, thereby contributing to impaired regulatory functioning. Controlled laboratory studies of total sleep deprivation (TSD) generally show alterations in physiological arousal and affective state, but the relationship of affect and emotion with physiological arousal during TSD has not been well characterized. Established methods for examining physiological arousal include electrodermal activity (EDA) measures such as non-specific skin conductance responses (NSSCR) and skin conductance level (SCL). These measures are robust physiological markers of sympathetic arousal and have been linked to changes in experienced emotion. To explore the link between physiological arousal and affect during sleep deprivation, we investigated individuals’ EDA under TSD and its relationship to self-reported affect. We also investigated the relationship of EDA to two other measures known to be particularly sensitive to the arousal-decreasing effects of TSD, i.e., self-reported sleepiness and performance on a vigilant attention task. Data were drawn from three previously published laboratory experiments where participants were randomly assigned to either well-rested control (WRC) or 38 h of TSD. In this data set, comprising one of the largest samples ever used in an investigation of TSD and EDA (N = 193 with 74 WRC and 119 TSD), we found the expected impairing effects of TSD on self-reported affect and sleepiness and on vigilant attention. Furthermore, we found that NSSCR, but not SCL, were sensitive to TSD, with significant systematic inter-individual differences. Across individuals, the change in frequency of NSSCR during TSD was not predictive of the effect of TSD on affect, sleepiness, or vigilant attention, nor was it related to these outcomes during the rested baseline. Our findings indicate that while physiological arousal, as measured by EDA, may be useful for assessing TSD-related changes in non-specific arousal at the group level, it is not associated with individuals’ self-reported affect at rest nor their change in affect during TSD. This suggests that an essential aspect of the relationship between physiological arousal and self-reported affect is not well captured by EDA as measured by NSSCR.