The key role of quinone substitution reactions in many biological processes, specifically anti-cancer activity of 1,4-naphthoquinones, makes the study of their reactivity towards nucleophiles essential. Here we studied the reactions of 2-methoxy-1,4-naphthoquinone and 2-bromo-3-methoxy-1,4-naphthoquinone with aminoalkylthiols, where two functional groups are both reactive. In the reaction with 2-aminoethanethiol, or 2-N-butylaminoethanethiol, 2-bromo-3-methyl-1,4-naphthoquinones in methanol yielded the cyclic product, 1-aza-4-thia-1,2,3,4-tetrahydroanthracene-9,10-diones, which indicate two functional groups are both involved in the reaction with 1,4-naphthoquinones. On the other hand, 2-methoxy-1,4-naphthoquinone in the reaction with 2-aminoethanethiols yielded 2-(2-aminoethylthio)-3-methoxy-1,4-naphthoquinones as the major product, along with the cyclic product, 1-aza-4-thia-1,2,3,4-tetrahydroanthracene-9,10-diones as a minor product. With N-methyl-2-mercaptoacetamide as an aminoalkylthiol, 2-methoxy-1,4-naphthoquinone and 2-bromo-3-methoxy-1,4-naphthoquinone both exclusively afford, N-methyl-2[2-(3-methoxy-1,4 naphthoquinonyl)]-thioacetamide as the consequence of single substitution step. Interestingly, in the same reactions in the presence of a base such as N-methylimidazole, disubstituted product, N-methyl-2-[2-(3-methylamino-1,4 naphthoquinonyl)]thioacetamide was isolated as the major product via the secondary reaction of the primary single substitution product with methylamine as the hydrolysis product of excess N-methylmercaptoacetamide.