Objective The aim of this study was to evaluate the adherence pattern to medications and the influence of non-adherence on hospitalization rate among Egyptian patients who were diagnosed with systemic lupus erythematosus (SLE). Methods This cross-sectional interview-based study was conducted in an Egyptian rheumatology outpatient clinic. Individuals with SLE who were prescribed oral medications were included in the study. The 19-item Compliance Questionnaire of Rheumatology (CQR) was employed to evaluate drug adherence. Patients were classified as non-adherent and adherent group based on their CQR score Sociodemographic variables, clinical and therapeutic data, and the frequency of outpatient visits and hospitalization were collected and compared between the two groups. Results In total, there were 161 SLE patients who participated in the study with mean age 30.70 ± 9.62 years, 129 females and 32 males (F:M 5.4:1). Of them, 93 patients were assigned to the non-adherent group, whereas 68 patients were assigned to the adherent group. There was a statistically significant difference in terms of marital status ( p = 0.009), employment ( p = 0.032), and the frequency of physical activity ( p = 0.045) between the two groups. The adherents had a higher rate of administration of antimalarials (88.2% vs 75.3%, p = 0.039). The frequency of recurrent fever was lower in adherents (23.5% vs 38.7%, p = 0.042), lymphadenopathy (11.8% vs 31.2%, p = 0.004), recurring oral ulcers (25% vs 50.5%, p = 0.001), and substantial hair loss (87.1% vs 98.5%, p = 0.009) in comparison to non-adherents. The number of yearly outpatient visits was considerably greater in adherents ( p = 0.007), while the number of prior hospitalizations was higher in non-adherents ( p < 0.001). Non-adherents believed that taking medicines disrupt patients’ daily routine ( p < 0.001) and were more afraid of the occurrence of an adverse drug reaction ( p < 0.001). Conclusions Egyptian SLE patients have an alarmingly high percentage of medication non-adherence. There is a strong association between medication non-adherence and frequency of hospitalization and cumulative clinical manifestations.