Systemic lupus erythematosus (SLE) might increase deep neck infection (DNI) risk, but evidence supporting this hypothesis is limited. In this retrospective follow-up study, the SLE-DNI association was investigated using data from the Registry for Catastrophic Illness Patients, which is a subset of the Taiwan National Health Insurance Research Database. All patients newly diagnosed as having SLE in 1997-2011 were identified, and every SLE patient was individually matched to four patients without SLE according to sex, age, and socioeconomic status. The study outcome was DNI occurrence. DNI treatment modalities and prognoses in SLE and non-SLE patients, along with the association of steroid dose with DNI risk, were also studied. In total, 17,426 SLE and 69,704 non-SLE patients were enrolled. Cumulative DNI incidence was significantly higher in the SLE cohort than in the non-SLE cohort (p < 0.001). The Cox regression model demonstrated that SLE significantly increased DNI risk (hazard ratio: 4.70; 95% confidence interval: 3.50-6.32, p < 0.001). Moreover, in the sensitivity and subgroup analyses, the effect of SLE on DNI was stable. Relatively few SLE-DNI patients received surgical interventions (15.6% vs. 28.6%, p = 0.033). The between-group differences in tracheostomy use and hospitalisation duration were nonsignificant. In SLE patients, high steroid doses significantly increased DNI incidence (≥3 vs. <3 mg/day = 2.21% vs. 0.52%, p < 0.001). This is the first study demonstrating that SLE increases DNI risk by approximately five times and that high steroid dose increases DNI incidence in SLE patients.