The fundamental concern of the full-depth reclamation (FDR) technique using Portland cement (FDR-PC) lies in its detrimental effect on the environment. Therefore, researchers are exploring alternative binders that are comparatively greener but compatible with FDR. This study evaluates both the strength and durability aspects of FDR incorporating geopolymer binder (FDR-GP) as an alternative to conventional FDR-PC. Various blends of fly ash (FA) and ground granulated blast furnace slag (GGBS) have been experimented with as geopolymer pre-cursors, ensuring that the additive content does not exceed 20% by weight of the total mix. Sodium hydroxide (NaOH) was utilized for the alkalinization in varying molarities to enhance the performance of the mixes. The experimental design was formulated to achieve a target 7-day unconfined compressive strength (UCS) strength of 4.95 MPa. This was obtained at a lower molarity (M) of 2 M and a 70% FA, 30% GGBS binder content. The mixes performed satisfactorily in both compression and flexure, along with excellent durability properties analyzed through wetting and drying tests. Furthermore, the long-term performance of FDR-GP mixes was investigated with regard to both UCS and flexural strength after 56, 161, and 238 days of curing. Thereafter, a comprehensive microstructural analysis was conducted to understand the fundamental changes in the matrix that influence mix performance. The outcome of this research confirms the potential of using FA/GGBS-based geopolymer as an alternative binder in FDR projects of flexible pavement, the mechanical and durability properties of which adequately satisfy the requirements as stipulated in various design standards.