During this investigation, both microstructural and fatigue analyses were carried out to determine the structural integrity of a flexible pavement system with a 4% cement-stabilised base course. Scanning electron microscope analyses as well as material characterisation studies, which included Texas triaxial, resonant-frequency, ultrasonic pulse, and accelerated load facility tests, were conducted to collect the requisite data. Additionally, dynamic finite element analyses were employed to determine the critical strains necessary to calculate the fatigue performance. Correlations between selected microstructural parameters and the fatigue performance of treated pavement structures were established by multilayer feed-forward neural networks. The results, which demonstrated a meaningful relationship between microstructural information and fatigue characteristics of a flexible pavement, may be used to predict the fatigue performance of such systems.