Patients with systemic lupus erythematosus (SLE) are known to have lower heart rate variability and impaired vagal modulation, and right lateral position has been shown to lead to a higher vagal modulation than supine position in healthy subjects and patients with cardiovascular diseases. This study evaluated the effect of disease activity and different recumbent positions on cardiac autonomic nervous modulation by heart rate variability analysis in patients with SLE. Thirty-five female patients with SLE and 33 female controls were enrolled in this study. Electrocardiogram was recorded during supine, left lateral, and right lateral positions for 15 min. Both time and frequency domains heart rate variability measures were calculated. The normalized high-frequency power was used as the index of vagal activity, and the low-/high-frequency power ratio as the index of sympathovagal balance. We found that patients with SLE had lower indices of time domain heart rate variability measures and lower low-frequency power, high-frequency power, and normalized high-frequency power than control subjects. SLE patients with lower serum albumin had lower normalized high-frequency power and higher low-/high-frequency power ratio. In patients with SLE, right lateral position could lead to higher high-frequency power, normalized high-frequency power, and lower low-/high-frequency power ratio than supine position. In addition, the lower the normalized high-frequency power in supine position the patient had, the greater the increase in normalized high-frequency power when the position of the patient was changed from supine to right lateral. Thus, serum albumin level might be used as a potential disease severity index of SLE, and right lateral position can lead to higher vagal modulation and lower sympathetic modulation, renin-angiotensin-aldosterone modulation, and vagal withdrawal than supine position in patients with SLE. Right lateral position can be used as an efficient and physiological vagal enhancer in SLE patients with depressed vagal modulation.