There are contradictory opinions if late-onset systemic lupus erythematosus (SLE) is associated with a different, more benign disease course and better prognosis than early-onset SLE. The objective of this study was to evaluate the clinical manifestations, course, treatment, and prognosis of late-onset SLE. Patients who developed SLE after/or at the age of 50 years were considered late-onset SLE and compared to a group of randomly selected patients aged younger than 50 years at the diagnosis, matched for disease duration. Lower frequency of cutaneous manifestations (p = 0.01) and higher frequency of cytopenias (p = 0.02) were registrated at the SLE onset in the late-onset group. Atypical clinical presentation of SLE contributed to a longer delay of diagnosis in late-onset SLE patients (p = 0.005), who fullfiled less American College of Rheumatology criteria at the diagnosis (p = 0.022). Cumulative incidence of clinical manifestations showed lower frequency of cutaneous (p = 0.017), neuropsychiatric manifestations (p = 0.021), lupus nephritis (p = 0.006), and higher frequency of Sjogren's syndrome (p = 0.025) in the late-onset group. Late-onset SLE patients received lower doses of corticosteroid (p = 0.006) and cyclophosphamide (p = 0.001) and had more cyclophosphamide-induced complications (p = 0.005). Higher prevalence of comorbid conditions in the late-onset group (p = 0.025), and higher Systemic Lupus International Collaborating Clinics/American College of Rheumatology damage index was noticed (p = 0.018). Despite the less major organ involvement and more benign course of disease, late-onset SLE has poorer prognosis, because of the higher frequency of comorbid conditions and higher organ damage, due to the aging and longer exposition to a classical vascular risk factors.