Delta neutrophil index (DNI) is a novel diagnostic and prognostic biomarker of various infectious or inflammatory conditions. However, data on optimal measurement time are scarce, and no studies have evaluated the potential role of the DNI as a prognostic biomarker of gastrointestinal diseases with diagnostic test accuracy meta-analysis. Core databases were searched. The inclusion criteria were as follows: patients who have gastrointestinal diseases and DNI measurements presenting diagnostic indices for predicting the prognosis, including severity, surgical outcomes, and mortality from gastrointestinal diseases. We identified twelve studies for the systematic review and ten studies for the quantitative analysis. Pooled area under the curve, sensitivity, specificity, and diagnostic odds ratio of DNI at the initial admission date were 0.82 (95% confidence interval: 0.78-0.85), 0.75 (0.52-0.89), 0.76 (0.63-0.86), and 10 (3-35), respectively. Meta-regression showed no reasons for heterogeneity and publication bias was not detected. Fagan's nomogram indicated that the posterior probability of 'poor prognosis' was 76% if the test was positive, and 'no poor prognosis' was 25% if the test was negative. The DNI can be considered as a reliable initial measurement biomarker for predicting prognosis in patients with gastrointestinal diseases.