Solvent effects on a potential energy surface crossing are investigated by optimizing a conical intersection (CI) in solution. To this end, the analytic energy gradient has been derived and implemented for the collinear spin-flip density functional theory (SFDFT) combined with the effective fragment potential (EFP) solvent model. The new method is applied to the azomethane-water cluster and the chromophore of green fluorescent protein in aqueous solution. These applications illustrate not only dramatic changes in the CI geometries but also strong stabilization of the CI in a polar solvent. Furthermore, the CI geometries obtained by the hybrid SFDFT/EFP scheme reproduce those by the full SFDFT, indicating that the SFDFT/EFP method is an efficient and promising approach for understanding nonadiabatic processes in solution.