The molecular hopping of a lone 3,4,9,10-perylenetetracarboxylic dianhydride (PTCDA) molecule adsorbed on a Ge(001) surface is studied by density functional theory calculations and the climbing-image nudged elastic band method, in which the PTCDA molecule moves along a trough between two adjacent Ge dimer rows. We confirm the previously reported stable state (SS) structure and determine the transition state (TS) structure during the hopping. The TS exhibits the following characteristic features: PTCDA is almost flat above the surface and the adsorption energy (−1.69 eV) is mostly due to the van der Waals (vdW) interaction. The hopping rate constant calculated from the Gibbs free energy of activation indicates that PTCDA is unlikely to hop at 500 K but likely to hop at about 700 K. From changes of Ge–O bond distances during the hopping, the mechanism is named an “inchworm/cheetah”-like hopping with concerted dimer flipping. The origin of the adsorption energy changes from the chemical interaction plus the vdW interaction at the SS to the vdW interaction at the TS during the hopping. The present study gives an insight that strongly adsorbed planar molecules with functional groups on reactive semiconductor surfaces are more mobile than expected.