Heat exchangers are essential components in energy generation systems, HVAC&R applications, chemical processes, and industrial waste heat recovery. However, fouling and pressure drop remain major challenges that reduce the efficiency of conventional heat exchangers and complicate their design. Despite extensive research on these issues, CFD-based assessments of vacuum-operated heat pipe heat exchangers under realistic dirty flue gas conditions and using different working fluids remain limited. In addition, the combined effects of fouling, pressure drop, and heat transfer have not been comprehensively examined in most previous studies. To address this gap, the present study investigates the thermal and hydrodynamic performance of a vacuum-operated refillable heat pipe heat exchanger designed for waste heat recovery from contaminated flue exhaust gases using Computational Fluid Dynamics (CFD). The novelty of the research lies in the detailed modelling of polluted flue gas conditions, the comparative evaluation of alternative working fluids within a unified framework, and the integrated assessment of fouling and pressure-drop effects on overall system performance. Furthermore, the study identifies optimal design parameters for industrial applications and demonstrates the energy recovery potential of heat pipe systems as a viable alternative to conventional heat exchangers. The CFD results indicate that the flow remains in the turbulent regime, promoting effective convective heat transfer throughout the system. The calculated Nusselt number and average convective heat transfer coefficient (h) confirm the high thermal performance of the heat pipe configuration. The findings show that vacuum-operated heat pipe heat exchangers can provide efficient heat transfer while maintaining low pressure losses under contaminated flue gas conditions. Consequently, these systems offer an effective and sustainable solution for industrial waste heat recovery. The results contribute valuable design guidelines for improving industrial energy efficiency and optimising the performance of waste heat recovery systems, highlighting the potential of heat pipe technology in demanding operating environments.