AASHTO Type III prestressed girder is one of the most widely used girder types to carry highway bridge decks. However, very few quantitative studies have been conducted to study the effect of span-to-depth ratio (L/d) on flexural behavior of AASHTO Type III prestressed girder-deck system via finite element analysis. This paper presents the results of numerical analysis investigating the effect of two primary variables (reinforcement ratio and span-to-depth ratio) on the flexural properties of AASHTO Type III prestressed girder using finite element software Abaqus. A detailed finite element analysis (FEA) model was developed and verified against the relevant experimental data performed by other researchers. The analytical results showed good agreement with the experimental results. Based on the verified FE model, analyses were performed using variables including three critical span-to-depth ratios (L/d) of 10, 15 and 20 and prestressing reinforcement ratios (ρ%) of 0.101, 0.126 and 0.151. Ultimate strength, stiffness, and ductility of the prestressed Type III girder were investigated. The nonlinear finite element results demonstrated that different span-to-depth ratios can significantly affect flexural performance. It was found that a higher span-to-depth ratio has a lower stiffness and ultimate strength than a lower span-to depth ratio. However, the ductility decreases with the increase of the span-to-depth ratio. In addition, under the effect of prestressing reinforcement ratio, the impact of span-to-depth ratio on flexural performance increases.