Background: Aflatoxin is one of the most important fungal toxins with documented hepatotoxic, teratogenic, and immunosuppressive properties. This mycotoxin is mainly produced by species of the genus Aspergillus in feed. Therefore, the application of compounds, which prevent complications of aflatoxins without losing feed quality, is highly beneficial. Objectives: This study aimed to determine the effect of the Echinacea purpurea L. essential oils on the regulation of the microbial population of the gastrointestinal tract and some blood factors of aflatoxin-fed zebrafish. Methods: Zebrafish were divided into four groups of 45 fish in three replicates: control (G1); G2, fish fed with feed containing 500 µg/kg E. purpurea L. essential oils; G3, fish fed with feed containing 500 µg/kg E. purpurea L. essential oil and 3 ppm aflatoxin B1(AFB1); and G4, fish fed with feed containing 3 ppm AFB1. The fish were fed with diets for 60 days. After this period, they were euthanized, blood was collected from the tail vein, and blood smears were prepared. Fish hepatopancreas were used to measure alanine aminotransferase, aspartate transaminase, and alkaline phosphatase enzymes with an auto-analyzer. Also, intestinal contents were cultured to evaluate microbial population. Results: Results showed that liver enzymes increased in the aflatoxin group (P<0.05), and concurrent use of the essential oil along with AFB1 reduced the liver enzymes compared with the AFB1-treated group. Moreover, AFB1 could convert the microbial population to pathogens. Differential blood counts in the G2 and G3 groups showed an increase in the percentages of neutrophils and thrombocytes. Conclusion: According to the results of this study, E. purpurea L. essential oils could reduce the adverse effects of chronic contamination with AFB1 in zebrafish. Nevertheless, more studies are needed to better understand the immunological function of E. purpurea L. in zebrafish and its mechanism of action against AFB1.