To ensure therapeutic equivalence between the long-acting injectable (LAI) products, additional PK metrics other than Cmax and AUC were considered necessary. However, regarding the selection of additional PK metrics for bioequivalence (BE) assessment of exenatide LAI, a discrepancy existed between EMA's and USFDA's product-specific guidance. The EMA recommends that both the maximum plasma concentration in the initial-release phase (Cmax,1) and the extended-release phase (Cmax,2) should be determined. Nevertheless, the USFDA recommends the use of the partial area under the curve (i.e., the area under the curve from week 4 to the last sampling point; pAUC4w-t). The focus of this study was to compare the sensitivity of different PK metrics, including Cmax,1, Cmax,2, pAUC4w-t, early and late pAUC metrics truncated at different time points (three, four, five, six and seven weeks), to formulation-related parameters and pharmacodynamic (PD) markers of glycemic control. A sensitivity analysis was conducted using the published PK/PD model of exenatide LAI. The results indicated that Cmax,1 and Cmax,2 exhibited comparable sensitivities. AUC4w-t was sensitive to changes in detecting the differences in formulation-related parameters and PD markers of glycemic control, but did not provide superior sensitivity performance compared to Cmax,1 and Cmax,2. Among all tested PK metrics, AUC7w-t was found to be the most sensitive. The optimal cut-off time point for the pAUC should be set at the time of maximum plasma concentration in the extended-release phase (approximately 6–7 weeks). These results may provide useful insights into the selection of appropriate PK metrics for BE determination of exenatide LAI.