Due to the material properties of glass fiber-reinforced polymer (GFRP), GFRP-concrete decks with effective connections are prone to brittle failure. The shear stiffness of connectors can change the composite action, thereby affecting the ductility of GFRP-concrete decks. To investigate the impact of shear connectors on flexural behavior, GFRP-concrete decks were analyzed by finite element methods. Firstly, the simple constitutive models for different shear connectors were examined. The finite element models considering the slip between the GFRP plate and the concrete were subsequently validated on the basis of the experimental results of two specimens with different shear connectors. Finally, the flexural performance of GFRP-concrete decks with different shear connectors was analyzed. The analysis revealed that the interface treatment can increase the bending stiffness of GFRP-concrete decks and reduce their maximum stress. Moreover, GFRP-concrete with mixed shear connectors can exhibit high bending stiffness in the serviceability stage and show significant deflection as a safety warning prior to failure, due to changes in shear connector stiffness.