Background/aims One of the opportunistic pathogens which cause serious problems in the human immune system is Toxoplasma gondii, with toxoplasma encephalitis (TE) seen in patients affected by it. The treatment of these patients is limited, and if not treated on time, death will be possible. Methods In this study, the effects of the treatment with different doses of fluconazole (FLZ) in combination with the current treatment of acute toxoplasmosis on reducing the mortality rate and the parasitic load in the murine model in vivo were studied. The mice were treated with different doses of fluconazole alone, sulfadiazine, and pyrimethamine plus fluconazole. A day after the end of the treatment and 1 day before death, the mice’s brains were collected, and after DNA extraction and molecular tests, the parasite burden was detected. Results This study showed that a 10-day treatment with 20 mg/kg of fluconazole combined with sulfadiazine and pyrimethamine 1.40 mg/kg per day affected acute toxoplasmosis and reduced the parasitic load significantly in brain tissues and also increased the survival rate of all mice in this group until the last day of the study, in contrast to other treatment groups. These results also indicate the positive effects of combined therapy on Toxoplasma gondii and the prevention of relapse. Conclusions Reducing the parasitic burden and increasing the survival rate were more effective against acute toxoplasmosis in the combined treatment of different doses of fluconazole with current treatments than current treatments without fluconazole. In other words, combination therapy with fluconazole plus pyrimethamine reduced the parasitic burden in the brain significantly, so it could be a replacement therapy in patients with intolerance sulfadiazine.