Fly ash based geopolymer stabilized base layers (FA-GB) are considered as stabilized pavement materials which have the potential to replace the conventional cement-treated base layers (CTB). The present study aims to carry out a comparative performance assessment of FA-GB and CTB under laboratory conditions. FA-GB considered in the present study were prepared at different molarities of alkali activator - 4 M, 6 M and 8 M, and was compared with CTB with 6% cement. Class C Fly Ash was used in the present investigation. Performance assessment of these mixes was carried out in terms of compaction characteristics, unconfined compressive strength (UCS), durability, indirect tensile strength (ITS), resilient modulus (Mr) and fatigue performance of the mixes. FA-GB with 6 M and 8 M exhibited nearly 50% higher UCS value than CTB, while the UCS of FA-GB with 4 M was marginally less than that of CTB. It was interesting to note that FA-GB required more time for strength gain when compared to CTB. However, the ITS and Mr of the FA-GB mixes were nearly twice that of CTB. Fatigue performance studies were carried out at stress ratios of 0.5, 0.65 & 0.8, and it was observed that CTB mixes exhibited comparatively lower fatigue life when compared with FA-GB. The observed fatigue performances were further used in this study for calculate the strain reduction below the stabilized base layers and also fatigue analysis provide the reliable estimates about the relative performance of the base layer mixes. It was found that the critical strain values decreased nearly 16-30% when CTB was replaced by the FA-GB prepared with 6 M.