Chamomile is a multi-purpose medicinal plant. It approved its anti-trypanosomal effect in vitro before. This work aimed to study its anti-trypanosomal effect in vivo. For this aim, 28 parasite-free rats were used, seven remained non-infected (control group (CG)), while the others were infected with Trypanosoma evansi and then equally divided into Trypanosoma Group (TG): didn`t receive any treatment. Diminazene aceturate group (DAG): treated with Diminazene aceturate (3.5 mg/kg) on days 0, 14, and 28.Chamomile group (CAG): treated with chamomile extract (1300 μl/kg) on days 0, 14, and 28. Blood samples were collected daily for monitoring the parasitemia and the clinicopathological parameters were estimated on days 0 and 49. Tissue sections were collected from the liver, kidney, heart, lung, spleen, and brain on day 49, stained, and histopathologically examined. Although, both treatments displayed a significant (P<0.05) amelioration of the parasitological and clinicopathological results. DAG suffered from a higher degree of oxidative stress than CAG and the microscopical examination of their organs showed intensive lesions similar to TG. While CAG clinicopathological parameters and histopathological results approximately were similar to CG. Creatine kinase, creatine kinase-MB, lactic dehydrogenase, and glutathione reductase had high sensitivity and negative predictive value, and moderate specificity, positive predictive value, and accuracy rate. Conclusion:  chamomile extract is an effective anti-trypanosomal drug. Creatine kinase, creatine kinase-MB, lactic dehydrogenase, and glutathione reductase are moderate markers for the disease diagnosis and its treatment evaluation.