Objective: Assessment of gastrointestinal and autonomic symptoms in patients with systemic sclerosis, and possible associations with gastric emptying rate. Methods: Participant and patient disease-related characteristics were collected. Gastrointestinal and autonomic symptoms were assessed by the UCLA-SCTC GIT 2.0 and COMPASS-31 questionnaires, respectively. Potentially confounding gastrointestinal medications were discontinued where possible. Gastric emptying was assessed using a non-radioactive 13C sodium acetate isotope, end-expiratory breath samples collected at baseline and then serial timepoints up to 120 min. Results: In total, 49 participants were studied: 17 with systemic sclerosis with variable gastrointestinal involvement, and healthy matched (n = 17) and non-matched controls (n = 15), the last to control for the impact of age rather than disease on gastric emptying and autonomic function. The total mean (range) UCLA GIT 2.0 questionnaire for patients with systemic sclerosis was 0.63 (0.0–1.5) and for both healthy matched and non-matched controls was 0.04 (0.0–0.2), and was higher in patients with systemic sclerosis across all domains. The total mean (range) COMPASS-31 score for patients with systemic sclerosis patients was 32.2 (0.0–54.9) and for healthy matched- and non-matched controls: 7.45 (0.0–24.9) and 4.25 (0.0–2.1), respectively, again higher for patients with systemic sclerosis across all domains. No association was observed between patients’ UCLA GIT 2.0 total score (s = −0.039, p = 0.38), total COMPASS 31 score (s = −0.108, p = 0.68), or COMPASS-31 GI domain (s = −0.051, p = 0.85) and gastric emptying rates. Conclusion: Gastrointestinal and autonomic symptoms are overrepresented in patients with systemic sclerosis but did not associate with gastric emptying rates.