In the present study, we reported the one-pot synthesis of S,S- and S,O-substituted 1,4-naphthoquinones, their structural studies, and investigation of their antioxidant activity. The multicomponent reactions of 2,3-dichloro-1,4-naphthoquinone with sulfur- and oxygen-containing nucleophiles were investigated to obtain highly functionalized S,S- and S,O-substituted 1,4-naphthoquinone derivatives. All new compounds were characterized on the basis of H-1, F-19, and C-13 nuclear magnetic resonance spectroscopy, mass spectrometry, and Fourier transform infrared spectroscopy. Crystal structure of 2,3-dihydro-2-(hydroxymethyl)naphtho[2,3-b]-1,4-oxathiin-5,10-dione was determined by X-ray diffraction method. The synthesized compounds were screened for their antioxidant capacity and free radical scavenging activity using the cupric reducing antioxidant capacity method and DPPH method, respectively. 3-Chloro-2-[3-(3-chloro-1,4-dihydro-1,4-dioxonaphthalen-2-yloxy)propylsulfanyl]-1,4-naphthoquinone shows the highest antioxidant capacity with 0.63 cupric reducing antioxidant capacity-trolox equivalent antioxidant capacity coefficient.