Atomically thin graphene is an ideal model system for studying nanoscale friction due to its intrinsic two-dimensional (2D) anisotropy. Furthermore, modulating its tribological properties could be an important milestone for graphene-based micro- and nanomechanical devices. Here, we report unexpectedly enhanced nanoscale friction on chemically modified graphene and a relevant theoretical analysis associated with flexural phonons. Ultrahigh vacuum friction force microscopy measurements show that nanoscale friction on the graphene surface increases by a factor of 6 after fluorination of the surface, while the adhesion force is slightly reduced. Density functional theory calculations show that the out-of-plane bending stiffness of graphene increases up to 4-fold after fluorination. Thus, the less compliant F-graphene exhibits more friction. This indicates that the mechanics of tip-to-graphene nanoscale friction would be characteristically different from that of conventional solid-on-solid contact and would be dominated by the out-of-plane bending stiffness of the chemically modified graphene. We propose that damping via flexural phonons could be a main source for frictional energy dissipation in 2D systems such as graphene.