An essential issue in graphene nanoelectronics is to engineer the carrier type and density and still preserve the unique band structure of graphene. We report the realization of high-quality graphene p-n junctions by noncovalent chemical functionalization. A generic scheme for the graphene p-n junction fabrication is established by combining the resist-free approach and spatially selective chemical modification process. The effectiveness of the chemical functionalization is systematically confirmed by surface topography and potential measurements, spatially resolved Raman spectroscopic imaging, and transport/magnetotransport measurements. The transport characteristics of graphene p-n junctions are presented with observations of high carrier mobilities, Fermi energy difference, and distinct quantum Hall plateaus. The chemical functionalization of graphene p-n junctions demonstrated in this study is believed to be a feasible scheme for modulating the doping level in graphene for future graphene-based nanoelectronics.