Background: Acquired complement deficiency can occur in the setting of autoimmune syndromes, such as systemic lupus erythematosus (SLE), with very low or, occasionally, undetectable C3 levels. Based on data from patients with inherited complement defects, a perceived risk for serious bacterial infection exists amongst patients with transiently low complement, but the degree of risk related to C3 level is unknown. Methods: We performed a retrospective study of all pediatric patients with an undetectable total complement activity or absent individual complement components measured at our institution from 2002 to 2018. We assessed annual rate of serious bacterial infection (SBI) defined as requiring hospitalization and/or parenteral antibiotics. Among included SLE patients, we assessed the 30-day probability of SBI for given C3 measurements using a logistic regression model to determine risk. Results: Acquired complement deficiency secondary to SLE-related disease [n=44] was the most common underlying diagnosis associated with depressed complement levels. While controlling for immunosuppression level and lupus nephritis diagnosis, our logistic regression analysis of pediatric patients with SLE showed low C3 level was temporally associated with having an SBI event. Even in patients with equivalent immunosuppression, patients with an SBI were found to have lower C3 levels preceding the infection relative to patients without SBI. Conclusion: Pediatric patients with the diagnosis of SLE can develop very low C3 levels that are independently associated with risk of serious bacterial infection. Patients prone to complement consumption may particularly be at risk.