Abstract: The geometric configuration of cis–trans isomers critically influences their biological activities, making the separation and configurational identification essential for efficacy evaluation. In this study, cis/trans-1,2,4-oxadiazole derivatives were synthesized and comprehensively characterized by nuclear magnetic resonance (NMR), Fourier transform infrared spectroscopy (FT-IR), high-resolution mass spectrometry (HRMS), and theoretical calculations. This approach enabled unambiguous identification and distinction of a pair of isomers, including cis-4-[2-(3-((1H-indol-3-yl)methyl)-1,2,4-oxadiazol-5-yl)vinyl]-N,N-dimethylaniline and its trans-configuration analogue. Anti-Toxoplasma gondii activity assessment demonstrated that the cis-isomer (compound 2, selectivity index SI = 1.50) exhibited higher activity than the trans-isomer (compound 1, SI = 0.92) and the positive control spiramycin (SI = 0.98), highlighting the importance of configurational separation and identification in drug research. This study deepens the understanding of configuration–activity relationships and provides new insights for developing highly selective anti-Toxoplasma agents.