Synthesis of new 1,4-naphthoquinone derivatives is important in terms of searching new biologically active substances. In particular, compounds with piperazine and thiol moiety in their structure, show a wide range of pharmacological activity such as anti-inflammatory, anticancer, anti-fungal, anti-bacterial, anti-allergic, apoptosis and radical scavenging activities. In this study, new amino- and thio(substituted) naphthoquinone derivatives were synthesized by the reaction of thiols and thioalcohols with four naphthoquinone compounds which were used as starting materials. The new compounds were purified by column chromatography. The structure of the compounds was confirmed by different spectroscopic techniques.