Diagnostic discrepancy, defined as different admission and discharge diagnoses, could be a potential source of diagnostic error. We evaluated whether acute kidney injury (AKI) in the elderly affected their risk for diagnostic discrepancy. Patients aged ≥60 years from the general medical wards were prospectively enrolled and divided according to AKI status upon admission, using the Kidney Disease Improving Global Outcomes (KDIGO) criteria. We compared their discharge and admission diagnoses and identified patients with a diagnostic discrepancy, using multiple logistic regression analysis to evaluate the relationship between initial AKI and the presence of a diagnostic discrepancy. A total of 188 participants (mean age, 77.9 years) were recruited. Regression analysis showed that initial AKI on admission was associated with a higher risk of diagnostic discrepancy upon discharge (odds ratio [OR] 3.3; p < 0.01). In contrast, higher AKI severity was also associated with an increased risk of diagnostic discrepancy (for KDIGO grade 1, 2, and 3; OR 2.92, 3.91, and 4.32; p = 0.04, 0.03, and 0.02, respectively), suggesting that initial AKI upon admission could be an important risk factor for diagnostic discrepancy. Consequently, reducing geriatric AKI might have the potential to reduce diagnostic discrepancy among these patients.