Positional obstructive sleep apnea (POSA) is a major phenotype of sleep apnea. Supine-predominant positional patients are frequently characterized by milder symptoms and less comorbidity due to a lower age, body mass index, and overall apnea-hypopnea index. However, the bradycardia-tachycardia pattern during apneic events is known to be more severe in the supine position, which could affect the cardiac regulation of positional patients. This study aims at characterizing nocturnal heart rate modulation in the presence of POSA in order to assess potential differences between positional and non-positional patients. Patients showing clinical symptoms of suffering from a sleep-related breathing disorder performed unsupervised portable polysomnography (PSG) and simultaneous nocturnal pulse oximetry (NPO) at home. Positional patients were identified according to the Amsterdam POSA classification (APOC) criteria. Pulse rate variability (PRV) recordings from the NPO readings were used to assess overnight cardiac modulation. Conventional cardiac indexes in the time and frequency domains were computed. Additionally, multiscale entropy (MSE) was used to investigate the nonlinear dynamics of the PRV recordings in POSA and non-POSA patients. A total of 129 patients (median age 56.0, interquartile range (IQR) 44.8–63.0 years, median body mass index (BMI) 27.7, IQR 26.0–31.3 kg/m2) were classified as POSA (37 APOC I, 77 APOC II, and 15 APOC III), while 104 subjects (median age 57.5, IQR 49.0–67.0 years, median BMI 29.8, IQR 26.6–34.7 kg/m2) comprised the non-POSA group. Overnight PRV recordings from positional patients showed significantly higher disorderliness than non-positional subjects in the smallest biological scales of the MSE profile (τ = 1: 0.25, IQR 0.20–0.31 vs. 0.22, IQR 0.18–0.27, p < 0.01) (τ = 2: 0.41, IQR 0.34–0.48 vs. 0.37, IQR 0.29–0.42, p < 0.01). According to our findings, nocturnal heart rate regulation is severely affected in POSA patients, suggesting increased cardiac imbalance due to predominant positional apneas.