This paper presents a robust air-to-fuel ratio (AFR) control algorithm for managing exhaust gas recirculation (EGR) systems. In order to handle production tolerance, deterioration and parameter-varying characteristics of the EGR system, quantitative feedback theory (QFT) is applied for designing the robust AFR control algorithm. A plant model of EGR system is approximated by the first order transfer function plus time-delay (FOPTD) model. EGR valve position and AFR of exhaust gas are used as input/output variables of the plant model. Through engine experiments, parameter uncertainty of the plant model is identified in a fixed engine operating point. Requirement specifications of robust stability and reference tracking performance are defined and these are fulfilled by the following steps: during loop shaping process, a PID controller is designed by using a nominal loop transmission function represented on Nichols chart. Then, the frequency response of closed-loop transfer function is used for designing a prefilter. It is validated that the proposed QFT-based AFR control algorithm successfully satisfy the requirements through experiments of various engine operating points.