Objective Evidence suggests low health literacy is prevalent in the United States and associated with worse clinical outcomes, yet few studies have investigated health literacy in systemic lupus erythematosus (SLE). The objective of this study was to determine the prevalence of low health literacy and numeracy in lupus patients and to examine its association with disease characteristics. Methods Patients with SLE were recruited from an academic center clinic. Participants completed in-person assessments of health literacy (Rapid Estimate of Adult Literacy in Medicine, REALM) and numeracy (Numeracy Understanding in Medicine Instrument Shortened Version, S-NUMi). Clinical disease activity measures were obtained, including urine protein to creatinine ratio (UPC), Systemic Lupus Erythematosus Disease Activity Index (SLEDAI) and physician global assessment (PhGA) scores. Results Ninety-five SLE patients participated in the study; 13% had low health literacy and 73% had limited health numeracy. Patients with lower health literacy and numeracy were more likely to be Black, have Medicaid insurance, and earn income <$50 K annually. In linear regression models, patients with limited health numeracy had, on average, PhGA scores 0.31 points higher (95% CI: 0.02, 0.60) than patients with adequate numeracy, after adjusting for race and age. No clinical outcomes were associated with health literacy. Conclusion In this exploratory study, we found SLE patients with low numeracy had higher disease activity. Our findings indicate that lower health literacy and numeracy are more common among Black and socioeconomically disadvantaged patients. Additional research will be needed to investigate the impact of health literacy on other outcomes and racial disparities in SLE.