Roadway construction is challenging since it is hard to control and there are many factors that might change the quality of the resulting roadway. Pavement thickness variation is one of those factors that varies due to poor construction practices. As it was observed that the variabilities in pavement thicknesses affect the overall flexible pavement performance, this research study examined the effect of the asphalt layers thickness variability on flexible pavement structural capacity and performance. Two non- destructive testing (NDT) devices, including Ground Penetrating Radar (GPR) and Falling Weight Deflectometer (FWD) were used in this study. Layer thicknesses were obtained using both extracted field cores and GPR, while FWD was utilized to back- calculate layers moduli using deflections measured on each pavement layer. The structural capacity, represented by the effective structural number (SNeff) of each roadway section, was calculated according to the AASHTO 1993 procedures, while pavement performance was evaluated using the MEPDG software for just the thinnest (5EB) and thickest (6WB) roadway sections. Two MEPDG runs were conducted for each roadway section which includes using the planned and as constructed thicknesses. Results revealed that the structural capacity of all roadway sections had a SNeff value greater than the designed SN; values calculated ranged from 7.0 to 10.31 because each section had a subgrade modulus and total pavement thickness that varied from others. Predicted performance results showed that the runs conducted using MEPDG software passed all indicators except the thermal cracking. Even though the two roadway sections failed by thermal cracking and passed other indicators, it was found that as the thickness of the AC layer increase, the predicted performance value of all distresses and IRI will decrease. Therefore, it was concluded that the thickness variability across all tested roadway sections in this research study did not affect the flexible pavement's structural capacity. However, the performance of tested roadway sections was impacted.