Chronic pain and dysautonomic symptoms deteriorate Systemic sclerosis (SSc) patients’ health-related quality of life with serious repercussions on social life and even on sleep. Heart Rate Variability (HRV) analysis can identify cardiovascular autonomic control impairment in subclinical condition. The aim of the present observational cross-sectional study was to assess the relationship between dysautonomic symptoms, quality of life status and cardiovascular autonomic profile. ECG and respiration were recorded at rest in 20 SSc patients. HRV analysis was performed using two different approaches: Linear spectral analysis and non-linear symbolic analysis. Pain was evaluated using the Numeric Rating Scale (NRS) and 3 questionnaires were administered for the evaluation of sleep quality (PSQI), mood tone (PHQ-9) and disability (HAQ). We found that sleep impairment was related to sympathetic predominance at rest measured as low-frequency/high-frequency ratio (LF/HF) (r = 0.48 and p = 0.033); poorer sleep quality was related to higher pain values (r = 0.48 and p = 0.034) and depressive symptoms (r = 0.82 and p < 0.01); higher pain scores were related to higher cardiovascular vagal modulation and higher disability indexes (r = 0.47 and p = 0.038 & r = 0.55 and p = 0.012, respectively). In conclusion dysautonomia and chronic pain showed a severe impact on sleep quality and disability with a consequent worsening of depressive symptom in our cohort of SSc patients.