The structure, bonding, and protonation of NCSeX and XNCSe (X = Me, F, Cl, Br) derivatives has been investigated at the B3LYP/6-311++G(3df,2p)//B3LYP/6-31+G(d,p) level of theory. Three different approaches, namely, ELF, AIM, and NBO indicate that three main factors are responsible for the enhanced stability of the selenocyanates with respect to the isoselenocyanates when the substituents are halogens, whereas for alkyl substituents, it is the other way around: (a) the Se-X (X = F, Cl, Br) bonds are much stronger than the Se-X (X = Me); (b) the N-X (X = F, Cl, Br) bonds are much weaker than the N-X (X = Me) ones; (c) on going from the selenocyanates to the isoselenocyanates, when the substituents are halogen atoms, there is a significant weakening of the CN bond, which becomes essentially a double bond, whereas upon methyl substitution the CN bond retains its triple bond character. The same stability trends are observed for the corresponding N-protonated species. More importantly, the calculated stability differences are rather similar to those obtained for the neutral compounds, so that selenocyanates and isoselenocyanates exhibit rather similar basicities in the gas phase. Both types of isomers behave as gas-phase nitrogen bases.