This paper presents the design of geosynthetic reinforced flexible pavements and their modification by incorporating waste materials into bonded and unbonded layers of the pavement structure. The optimal design of flexible pavements was achieved by minimizing the construction cost of the pavement. The incorporation of waste materials into the pavement structure affects the material properties. Therefore, along with the traffic load, the effects of the material properties of the asphalt concrete, base layer, sub-base layer, and subgrade were analyzed in terms of pavement structure costs and CO2 emissions of materials used in pavement construction. In addition, a comparison was made between pavements with and without geosynthetic reinforcement in terms of design, optimum construction cost, and CO2 emissions. The use of geosynthetics is even more effective in pavement structures that contain waste materials in an unbound layer, both in terms of cost and CO2 emissions. The minimum value of the California Bearing Ratio of the subgrade was determined at which the use of geosynthetic reinforcement for pavement structure with and without the inclusion of waste materials is economically and sustainably justified. The use of geosynthetics could result in a 15% reduction in pavement structure cost and a 9% reduction in CO2 emissions due to the reduced thickness of unbound layers. In addition, reducing the CBR of the unbound layer from 100% to 30% due to the inclusion of waste materials implies a cost increase of up to 13%. While the present study is based on an empirical pavement design method in which pavement thickness is limited by the pavement thickness index, the same minimum thicknesses are obtained in the optimization process regardless of whether the objective function is the minimum construction cost or minimum CO2 emissions.