Background: Both preterm birth and sleep disordered breathing (SDB) affect sleep in children. We compared the effects of SDB on sleep macro-architecture and micro-architecture in children born preterm (N = 50) and children born at term (N = 50). We hypothesized that sleep would be more disrupted in children born preterm. Methods: Polysomnographic studies matched for age (3–12 years) and SDB severity were analyzed. Sleep macro-architecture was assessed using standard criteria and micro-architecture was evaluated using spectral analysis of the electroencephalogram and slow wave activity (SWA) calculated for each sleep stage across the night. Results: Ex-preterm children (gestational age 29.3 ± 3.6 weeks, mean ± standard error of the mean) were not different from controls for demographic or respiratory parameters or sleep macro-architecture. Theta power in N2 tended to be higher for F4 (p < 0.05) and C4 (p < 0.07). In the second non-rapid eye movement period, SWA was significantly higher in the preterm group compared to the term group for both F4 and C4 (p < 0.05 for both). Conclusions: Sleep micro-architecture in children born preterm showed increased theta power and SWA. These differences provide evidence of increased sleep debt and reduced dissipation of sleep debt across the night. Further studies are required to identify if these findings are related to impaired neurocognition and behavior.