This paper presents a modeling study based on finite element (FE) analysis to mechanistically evaluate flexible pavements constructed with quarry by-products (QB). Twelve pavement test sections, a control section, and 11 others incorporating QB as unbound subgrade replacement and chemically stabilized base/subbase applications were evaluated for field performance using accelerated pavement testing (APT). First, falling weight deflectometer (FWD) deflection basin parameters were calculated and compared with critical pavement responses to evaluate the structural adequacies of the QB pavement sections. The moduli of the constructed pavement layers were then backcalculated from the FWD deflections using the GT-PAVE FE analysis program with nonlinear and cross-anisotropic layer characterizations. For stabilized QB applications, the layer properties calculated from this analysis for the base/subbase layers were used to calculate critical pavement responses. The sections were compared using a response benefit parameter, defined as the ratio of maximum resilient surface deflection in a conventional pavement, as the control section, to that obtained for each section having a certain QB application in consideration. According to the results obtained from the APT sections and the mechanistic FE analyses, the measured and calculated FWD deflection basins were successfully matched with individual sensor errors not exceeding 5% for all 12 test sections. The calculated response benefits indicated significant advantages for using cement-stabilized QB applications over fly ash-stabilized QB applications and conventional flexible pavement sections. Considering the pavement structural response benefits and good performance trends observed, major cost benefits can be realized by routine use of these sustainable QB applications.