Four new series of arctigenin derivatives were designed, synthesised, and evaluated for their anti-Toxoplasma gondii activity in vitro and in vivo. Among the synthesised compounds, 4-(3,4-dimethoxybenzyl)-3-(4-((1-(2-fluorobenzyl)-1H- 1,2,3-triazol-4-yl)methoxy)-3-methoxybenzyl)dihydrofuran-2(3H)-one (D4) exhibited the most potent anti-T. gondii activity and low cytotoxicity (IC50 in T. gondii: 17.1 μM; IC50 in HeLa cells: ≥ 600.0 μM; Selectivity: 35.09), demonstrating better results than the lead compound arctigenin (IC50 in T. gondii: 586.4 μM; IC50 in HeLa cells: 572.7 μM; Selectivity: 0.98) and the clinically applied positive-control drug spiramycin (IC50 in T. gondi: 262.2 μM; IC50 in HeLa cells: 189.0 μM; Selectivity: 0.72) in vitro. Furthermore, 2-(4-((4-(3,4-dimethoxybenzyl)-2-oxotetrahydrofuran-3-yl)methyl)-2- methoxyphenoxy)N-phenylacetamide (E5) had better inhibitory effects on T. gondii in vivo than spiramycin did. Compound D4 and E5 not only significantly reduced the number of tachyzoites in the peritoneal cavity of mice, but also resulted in their partial malformation (P < 0.05) in vivo. The determination of liver and spleen index and biochemical parameters, such as alanine aminotransferase (ALT), aspartate aminotransferase (AST), glutathione (GSH) and malondialdehyde (MDA), were comprehensively evaluated for compound D4 and E5's anti-T. gondii activity and some damage to the liver. In addition, the results of a docking study of D4 into the T. gondii calcium-dependent protein kinase 1 (TgCDPK1) receptor protein-binding site revealed that its mode of action was possibly as a TgCDPK1 inhibitor. Overall, the results revealed that D4 and E5 are promising lead compounds for the further development and identification of arctigenin derivatives as anti-T. gondii agents.