Variable geometry turbocharger and exhaust gas recirculation valves are widely installed on diesel engines to allow optimized control of intake air mass flow and exhaust gas recirculation ratio. The positions of variable geometry turbocharger vanes and exhaust gas recirculation valve are predominantly regulated by dual-loop proportional–integral–derivative controllers to achieve predefined set-points of intake air pressure and exhaust gas recirculation mass flow. The setpoints are determined by extensive mapping of the intake air pressure and exhaust gas recirculation mass flow against various engine speeds and loads concerning engine performance and emissions. However, due to the inherent nonlinearities of diesel engines and the strong interferences between variable geometry turbocharger and exhaust gas recirculation, an extensive map of gains for the P, I, and D terms of the proportional–integral–derivative controllers is required to achieve desired control performance. The present simulation study proposes a novel fuzzy logic control scheme to determine appropriate positions of variable geometry turbocharger vanes and exhaust gas recirculation valve in realtime. Once determined, the actual positions of the vanes and valve are regulated by two local proportional–integral– derivative controllers. The fuzzy logic control rules are derived based on an understanding of the interactions among the variable geometry turbocharger, exhaust gas recirculation, and diesel engine. The results obtained from an experimentally validated one-dimensional transient diesel engine model showed that the proposed fuzzy logic control scheme is capable of efficiently optimizing variable geometry turbocharger and exhaust gas recirculation positions under transient engine operating conditions in real-time. Compared to the baseline proportional–integral–derivative controllers approach, both engine’s efficiency and total turbo efficiency have been improved by the proposed fuzzy logic control scheme while NOx and soot emissions have been significantly reduced by 34% and 82%, respectively.