Introduction: Systemic lupus erythematosus (SLE) reduces the health-related quality of life (HRQoL), even during periods of disease quiescence. We investigated whether subclinical inflammation as reflected by cytokine levels is linked with reduced HRQoL. Methods: A cross-sectional study of SLE patients (n = 52, mean age 47.3, 86.5% female) who completed a Short Form Health Survey-36 (SF-36) questionnaire. The clinical and demographic data, scores for the disease activity (SLEDAI-2K), organ damage (SDI), and laboratory data were collected simultaneously. The autoantibody and cytokine levels (IFN-γ, IL-1β, IL-4, IL-6, IL-10, IL-12, IL-17, BAFF, TNF-α, TGF-β1, MIP-1α, MIP-1β and MCP-1 (levels in pg/mL) were quantified by sandwich ELISA. The comparisons and associations were assessed non-parametrically, and a multiple regression determined the effect sizes (ES) of the variables on the SF-36 domain and summary scores. Results: The SF-36 summary and domain scores for SLE patients were significantly (20–40%) lower than in a comparable control group, with the exception of the Mental Health scores (p = 0.06). SLE patients had a normal body mass index (BMI) (median, 24.2 kg/m2), a high rate of smoking (69.2%), and usage of social security benefits (90.4%). TGF-β1 (ES 0.06), IL-12 (ES −0.11), IFN-γ (ES 0.07) and MCP-1 (ES 0.06) influenced the SF-36 domain scores; and MCP-1 (ES 0.04) influenced the Mental Health Summary Score (MCS). Obvious manifestations, including patient visual analogue scale (VAS) (ES −2.84 to −6.29), alopecia (ES −14.89), malar rash (ES −14.26), and analgesic requirement (ES −19.38), independently influenced the SF-36 items; however, the SF-36 scores were not reflected by the physician VAS or disease activity (SLEDAI-2K). Conclusions: Cytokines had a minimal impact on HRQoL in SLE patients, especially compared to visible skin manifestations, central nervous system (CNS) damage, and pain. Better tools are needed to capture HRQoL in measures of disease activity.