The adsorption of thiophene on Si(111)–7×7 has been studied with scanning tunneling microscopy (STM) and kinetic Monte Carlo (kMC) modelling. Previous experimental studies of this system clearly demonstrated that thiophene prefers to chemisorb on the faulted half of the 7×7 unit cell. The STM studies reported here concur with this and provide further information about thiophene site preference as a function of coverage. Additionally, an ab initio theoretical investigation of this system demonstrated that the occupancy of available adsorption sites could not be explained using equilibrium binding energies, as these were calculated to be the same for all experimentally identified adsorption sites (≈1.0 eV). To investigate the possibility that site selection is kinetically controlled, a kMC model was developed. This model places the molecule in a mobile precursor state, allowing the molecule to traverse the surface before chemisorbing. The kMC model was found to reproduce the STM data, providing compelling evidence that site occupancy in this system is indeed kinetically controlled at room temperature. Activation energy differences, for each the four unique chemisorption geometries, could be extracted from a fit of the kMC model predictions to the experimental data (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)