Metronidazole (MTZ) was the most widely accepted treatment for Blastocystis hominis (B. hominis) with high treatment failure rate, resistance and potential mutagenic and carcinogenic effects so there is urgent need to find out new, effective and safe treatment against B. hominis. The present research aimed to evaluate the therapeutic effect of the aqueous extract of Nigella sativa (NS) at different doses on B. hominis in vitro and in vivo in comparison to MTZ as a control drug. Isolates of B. hominis were obtained from patients complaining of diarrhea and abdominal pain. Isolates were cultured in egg diphasic medium (LE) for in vitro study and to adjust proper inoculating dose for in vivo study. The aqueous extract of NS at concentrations of 100 & 500 µg/ml showed a potent lethal effect on B. hominis isolates in vitro. Caecal tissue of experimentally infected and treated mice with two different doses of NS (250 & 500 mg/kg/d) were examined histopathologically and compared with that of mice infected and treated by two doses of MTZ (62 & 125 mg/kg/d) as control drug and Infected untreated mice as negative control group. Histopathological examination of infected untreated group showed all pathological degrees in the caecal tissue while infected treated one showed remission of pathological changes especially with higher dose (500 mg/kg). Present study proved that N. sativa had inhibitory effect on B. hominis in vitro and prevented cytopathic effect in infected mice inoculated orally with B. hominis.