Exhaust gas recirculation (EGR) is an important feature targeted on NOx emission reduction in modern marine internal combustion engines. Its capabilities are, however, often compromised due to inability of overcoming large scavenging pressure drop. This article targets at a control system design for a so-called high pressure EGR system, where the recirculated exhaust gas flow is boosted via additional turbocharger mounted in the feedback piping. The EGR fraction is typically hard to measure and requires a number of additional sensors installed. Therefore, we address this problem by designing a nonlinear (unscented Kalman) filter capable of estimating the recirculated exhaust gas fraction based on two measurements, easily available from manifold absolute pressure (MAP) and variable geometry turbocharger (VGT) shaft speed sensors. The control objective in this application is to track the EGR fraction, which we achieve by utilizing the second-order sliding mode controller (super-twisting algorithm), known for its nonlinear and robust nature. The certainty equivalence principle is used for the control design.