Measurement of the ratio between glycated hemoglobin (HbA1c) and total hemoglobin (Hb) is now recommended for screening and diagnosing diabetes, in addition to monitoring long-term glycemic control for patient management. The costly and time-consuming traditional assay methods, which involve multi-step, bench-top, and antibody-based immunoassays, have presented major challenges to their clinical utility. In this study, an integrated microfluidic system capable of rapidly measuring the level of HbA1c and Hb in an automated fashion was reported. Moreover, this detection assay used nucleic acid aptamers that exhibited high sensitivity and specificity to Hb and HbA1c to further enhance the robustness of the assay. Combining the advantages of microfluidics and aptamers, this system presents a promising tool for clinical diagnosis and management of diabetes. As a demonstration of its clinical utility, we analyzed patient whole blood samples with clinically-relevant concentrations of HbA1c and Hb (4.4%-12.5% and 12.1 g/dL-14.9 g/dL, respectively) on our integrated microfluidic system.