Background Hospitalizations due to systemic lupus erythematosus (SLE) incur substantial resource use. Hospitalization trends provide a key benchmark of the disease burden. However, there is little long-term data in Mexico. Therefore, we evaluated Mexican hospitalization trends for SLE during 2000–2019. Methods Hospitalization trends of SLE were studied using data from 2000 to 2019 releases of the National Dynamic Cubes of the General Direction of Health Information, which provides data on hospitalization discharges in Mexico. Patients aged ≥15 years hospitalized during the study period with a principal discharge diagnosis of SLE (ICD-10 code M32) were included. Results From 2000 to 2019, there were 17,081 hospitalizations for SLE, of which 87.6% were in females and 87% in subjects aged 15–44 years. From 2000 to 2019, the age-standardized hospitalization rate for patients with SLE increased from 0.38 per 100,000 persons to 0.65 per 100,000 persons with an average annual percentage change (APC) of 2.9% (95% CI 6.2–63.2). Although there was a significant uptrend from 2000 through 2011, there was a significant decline from 2011 to 2019 (APC: −4.8%, 95% CI −7.0% to −2.5%). Similar trends were identified in subjects aged 15–44 years and in both sexes. The length of stay and inpatient mortality decreased between 2000–2009 and 2010–2019. Conclusions Although there was a substantial increase in SLE hospitalizations in 2000–2019, in 2011–2019, a decreased trend was reported in younger patients and in females and males. The length of stay was also reduced.