No studies have evaluated the dynamic, time-varying relationship between delta electroencephalographic (EEG) sleep and high frequency heart rate variability (HF-HRV) in women. Delta EEG and HF-HRV were measured during sleep in 197 midlife women (M(age) = 52.1, SD = 2.2). Delta EEG-HF-HRV correlations in nonrapid eye movement (NREM) sleep were modeled as whole-night averages and as continuous functions of time. The whole-night delta EEG-HF-HRV correlation was positive. The strongest correlations were observed during the first NREM sleep period preceding and following peak delta power. Time-varying correlations between delta EEG-HF-HRV were stronger in participants with sleep-disordered breathing and self-reported insomnia compared to healthy controls. The dynamic interplay between sleep and autonomic activity can be modeled across the night to examine within- and between-participant differences including individuals with and without sleep disorders.