The reaction of acenaphthylene (ACN) with the Si(001) surface has been explored by means of density functional cluster model calculations. We have considered seven reasonable bonding configurations for the addition of ACN on the Si=Si surface dimer, and we found that the isomer with the ACN bound through the 1,2-alkene unit is the most thermodynamically stable. Among the remaining isomers, we have found the one deriving from a [4+2] addition on the Si(001) surface of the naphthalene unit of ACN significantly favored over the remaining ones. We considered the mechanism of ACN adsorption by characterizing the key intermediates of this process, i.e., a T complex precursor and a singlet diradical, for the formation of all the thermodynamically stable isomers. Our results show that also kinetics factors contribute to the high selectivity of the adsorption process and are consistent with recent experimental data, evidencing that ACN binds to the Si(001) surface mostly through the 1,2-alkene unit, whereas a small fraction binds through the naphthalene portion.