2,3-Dialkynylthiophene derivatives were synthesized by using regio- and stereocontrolled Pd-catalyzed Sonogashira coupling and desilylation reactions. The synthesized compounds were analyzed in silico for their pharmacokinetic parameters, general toxicity, and drug scores. In particular, 3-ethynyl-2-(phenylethynyl)-thiophene and 3-ethynyl-2-[(4-methylphenyl)ethynyl]thiophene were found to have relatively high drug scores and low toxicities. The antioxidant activity of the title compounds were evaluated by five different assays. 3-Ethynyl-2-(naphthalen-1-ylethynyl)thiophene displayed significant reducing and free radical scavenging activities.