Introduction Systemic Lupus Erythematosus (SLE) is a chronic multi-systemic autoimmune disease that mainly affects young females. SLE’s chronicity and high level of complications yield frequent clinic visitations & hospital admissions, increasing the necessity to investigate the healthcare system and improve patient satisfaction and quality of life. Objective This study aimed to understand SLE patients’ points of view on the healthcare system in Jordan, especially given the chronic nature of the disease. With a clearer understanding, improvements can be made to benefit both the patients and the healthcare system. Methods A cross-sectional study of 79 patients following up at the University of Jordan Hospital, rheumatology clinics were interviewed over the phone. Result The majority of patients were satisfied overall with the treatment services and medications as rated on a Likert scale of 1-5 (4.28 ± 1.01 and 4.19 ± 0.96, respectively) despite a quarter of patients complaining of adverse effects from the medications. The use of oral corticosteroids was significantly associated with a lower General Satisfaction Rate ( p = 0.050), while high income (1000 Jordanian Dinars and above) and fatigue contributed to a lower Medication Satisfaction Rate ( p = 0.016 and 0.000, respectively). A good physician-patient relationship was the most commonly cited reason for general satisfaction (73.4%) and was positively associated with the general ( p = 0.000) and medication satisfaction ( p = 0.004) rates. Conclusion SLE patients perceived high satisfaction rates despite adverse effects and symptoms. These higher satisfaction rates were seen predominantly due to good physician-patient relationships.