Purpose: As consequences of industrial processes, air pollution has led to increased cardiovascular diseases resulting in mortality. However, there are few pieces of evidence expressing physical fitness and gender impacts in such environments. Regarding long-term exposure to air pollution, this study aimed to determine the effect of physical fitness on post-exercise cardiac parasympathetic reactivation among healthy males and females. Methods: 120 individuals (46 ± 5 years) participated and were categorized into two main groups (n = 60; EG, CG); (1) The experimental group included individuals living in an air-polluted environment; (2) The control group included the citizens of a clean air region; and two physical fitness status subgroups (n = 30; active vs. sedentary) across both sexes. The heart rate (HR) changes at different timing after performing an incremental exercise, and T30 were calculated as metrics of cardiac parasympathetic reactivation. Results: The heart rate recovery values were substantially lower in EG in comparison to CG (p < 0.001) at different timing, while, T30 was significantly greater in residents of the air-polluted city compared to CG (p < 0.001). As for heart rate recovery at the 5th minute, the values were significantly lower in the steady-female group in comparison to the active females living in the air-polluted city (p < 0.01). Conclusion: Based on our findings, although physical fitness modifies the adverse impacts of long-term exposure to air pollution on post-exercise cardio-parasympathetic reactivation, it appears to parallel the acute/intermediate recovery of the thermoregulatory and vascular systems, among both sexes, it does not prevent them.