Swelling is one of the distresses that affect the pavement condition index (PCI) of airport runways. In northwest Queensland, swelling was observed in three different runways where sealed flexible pavement runways were deformed by the heaving of the expansive clay subgrades due to water intrusion. In the study, the trends of moisture content (MC) and corresponding swelling of these expansive soils were observed at different times. Subsequently, the PCI was calculated for the swelling of these runways using PAVER software. A correlation has been developed between swelling of different severity levels and the corresponding PCI. In addition, the relationship between MC and PCI has been established to demonstrate the influence of MC on the swell behavior, and the influence of seasonal MC variations on PCI was also examined. Finally, the study generated empirical equations to predict the swelling effects on the PCI and subsequent functional performance of the runway pavements constructed on expansive soils. A good correlation has been achieved between the swell parameter and the PCI. The correlation coefficient of determination Rjats:sup2</jats:sup> is computed to be 0.9981, 0.999, and 0.9987 for low, medium, and high severity of the swelling, respectively. The equations fitted with the experimental data well, which demonstrates the reliability of the empirical equations. From the result of swelling against MC and calculated PCI, it is evident that adverse effects are inevitable when water intrusion occurs in swelling soil subgrade. This high plasticity soil can deteriorate pavement performance and cause early pavement damage if allowed to swell.