Mass spectrometry analysis of 2-(acylamino)-1,4-naphthoquinone derivatives was carried out using electrospray ionization ion source in combination with tandem mass spectrometry. Protonated molecules were dissociated by application of the collision-induced dissociation (CID), and the protonation sites were suggested on the basis of the HOMO, molecular electrostatic potential map (MEP), proton affinity, and Fukui functions calculated by B3LYP/6-31+G(d,p). The main fragmentation mechanisms undergone by the protonated ions were elucidated on the basis of energy, geometry, and topology analysis of equilibrium geometries. Compounds exhibiting only aliphatic hydrogens at the lateral chain undergo interesting ketene elimination. On the other hand, only the benzoylium ion formation is detected for 2-benzoylamino-1,4-naphthoquinone. The bonds geometric and atoms in molecules parameters give evidence that acidic hydrogen atoms play an important role in the fragmentation pathways.