The identification of novel, easily measurable biomarkers of inflammation might enhance the diagnosis and management of immunological diseases (IDs). We conducted a systematic review and meta-analysis to investigate an emerging biomarker derived from the full blood count, the systemic inflammation index (SII), in patients with IDs and healthy controls. We searched Scopus, PubMed, and Web of Science from inception to 12 December 2023 for relevant articles and evaluated the risk of bias and the certainty of evidence using the Joanna Briggs Checklist and the Grades of Recommendation, Assessment, Development, and Evaluation Working Group system, respectively. In 16 eligible studies, patients with IDs had a significantly higher SII when compared to controls (standard mean difference, SMD = 1.08, 95% CI 0.75 to 1.41, p < 0.001; I = 96.2%, p < 0.001; moderate certainty of evidence). The pooled area under the curve (AUC) for diagnostic accuracy was 0.85 (95% CI 0.82-0.88). In subgroup analysis, the effect size was significant across different types of ID, barring systemic lupus erythematosus (p = 0.20). In further analyses, the SII was significantly higher in ID patients with active disease vs. those in remission (SMD = 0.81, 95% CI 0.34-1.27, p < 0.001; I = 93.6%, p < 0.001; moderate certainty of evidence). The pooled AUC was 0.74 (95% CI 0.70-0.78). Our study suggests that the SII can effectively discriminate between subjects with and without IDs and between ID patients with and without active disease. Prospective studies are warranted to determine whether the SII can enhance the diagnosis of IDs in routine practice. (PROSPERO registration number: CRD42023493142).