Successful sleep onset and maintenance is associated with a reduction in core temperature, facilitated by heat loss at the distal periphery. Problems with initiating and maintaining sleep in children with eczema may relate to impaired thermoregulatory mechanisms, which also contribute to itching and scratching. Our hypothesis was that nocturnal distal skin temperature in eczematous children would be lower than controls, and would also be related to poor sleep quality. We compared overnight polysomnography and distal (finger) and proximal (clavicle) skin temperature in 18 children with eczema and 15 controls (6–16 years). Children with eczema had longer periods of nocturnal wakefulness (mean [SD] = 88.8 [25.8] vs. 44.3 [35.6] min) and lower distal temperatures (34.1 [0.6] °C vs. 34.7 [0.4] °C) than controls, whereas proximal temperature and the distal–proximal gradient were not significantly different. In children with eczema, a higher distal temperature was associated with indicators of poor sleep quality, whereas lower distal temperature was related to more scratching events during sleep. In conclusion, our findings indicate complex interrelationships among eczema, thermoregulation and sleep, and further, that deficits in thermoregulatory mechanisms may contribute to sleep disturbances in children with eczema.