The objective of the present study was to assess the diagnostic value of urine, serum and plasma neutrophil gelatinase-associated lipocalin (NGAL) for the early diagnosis of acute kidney injury (AKI) among patients with suspected sepsis. Therefore, a meta-analysis was carried out to evaluate diagnostic accuracy data from the literature regarding the diagnosis of AKI in patients with sepsis. Electronic databases were systematically searched for relevant studies and quality assessment was conducted using the Quality Assessment for Diagnostic Accuracy Studies 2 tool. A summary receiver operating characteristic curve analysis was performed, and several parameters including sensitivity, specificity, diagnosis odds ratio (DOR) and area under the curve (AUC) were calculated to evaluate the diagnostic performance of urine, serum and plasma NGAL. Meta-regression, sensitivity and subgroup analysis were also conducted to identify the source of heterogeneity in the eligible studies. In total, 28 studies were included. The pooled sensitivities for urine, serum and plasma NGAL were 0.87, 0.83 and 0.80, respectively. Pooled specificity was 0.84, 0.79 and 0.74. The DORs were 35, 18 and 11, respectively. The AUC for urine, serum and plasma NGAL were 0.92, 0.87 and 0.84, respectively. Urine NGAL presented superior performance for the diagnosis of AKI with the highest AUC and other diagnostic accuracy values, compared with serum and plasma NGAL. Further studies are needed to clarify the controversial issue between the usefulness of serum and plasma NGAL.