Ethnopharmacological relevance Toxoplasma gondii is a protozoan parasite that infects many warm-blooded animals, including humans. The genus Eucalyptus has been used for centuries, particularly in traditional medicine, for its antimicrobial and anti-inflammatory properties. Aim of the study The phytochemical composition of Eucalyptus torquata buds extract was profiled and its potential to mitigate toxoplasmosis-related symptoms, counter histopathological insults, and inhibit cyst development in a mice model were investigated. Materials and methods HPLC-MS/MS was used to identify and annotate the phytochemical contents. Protective effects against acute and chronic toxoplasma infection were evaluated. Several biochemical parameters were tested, including AST and ALT, along with histopathological and immunohistochemistry assays. Molecular docking was utilized to pinpoint the compounds associated with the anti-toxoplasmosis activity. Results HPLC-MS/MS analysis revealed that the plant extract contained 61 secondary metabolites belonging to various polyphenols and organic acids. Administration of E. torquata extract at 200 and 400 mg/kg/day for 14 consecutive days to mice initially infected with T. gondii ME-49 strain significantly prolonged the survival time compared to the untreated and spiramycin-treated groups. In addition, the extract, especially at 400 mg/kg, reduced the brain cyst burden (53 % and 75 %) and viability (38 % and 43 %), and decreased animals’ mortality rates in both acute (48th-day post-infection) and chronic (64th-day post-infection) phases. Monitoring liver and renal function revealed that the extract counteracted the infection-induced damage. It significantly reduced AST, ALT, and creatinine levels and increased the serum albumin level compared to the untreated mice. Furthermore, the extract-treated mice groups showed a substantial reduction in neuron degeneration, hepatic necrosis, and the associated inflammatory signs. Immunohistochemical analyses of the cytoplasmic inducible nitric oxide synthase (iNOS) in brain and liver tissues showed that both the extract and spiramycin elicited significant decreases in iNOS expression in acute and chronic phases. Molecular docking suggested that epigallocatechin-epigallocatechin, gallic acid coumaroyl gallate, gallic acid shikimate, and galloyl diglucose had the most favorable binding affinities towards iNOS enzyme. Conclusion Altogether, these findings open a promising avenue into the potential role of E. torquata phytochemicals in managing toxoplasmosis and the related complications.