Angiogenesis and hemodynamic instability created by the irregular blood vessels causes hypoperfusion and angiogenesis‐mediated diseases. Therefore, therapies focusing on controlling angiogenesis will be a valuable approach to treat a broad spectrum of diseases. In this study, we explored the anti‐angiogenic potential of berberine (BBR) and also analyzed blood flow hemodynamics using zebrafish embryos. Zebrafish embryos treated with BBR (0.01–0.75 mM) at various doses at 1 hour post‐fertilization (hpf) developed a variety of phenotypic variations including aberrant blood vessels, tail bending, edema, and hemorrhage. Survival rates were much lower at higher dosages, and hatching rates were almost 99%, whereas control group appeared normal. Heart rate is an essential measure that has a strong association with hemodynamics. We used ImageJ software to study the heart rate of embryos treated with BBR, preceded by video processing. The resultant graph shows a significant decrease in heart rate of embryos treated with BBR in dose‐dependent manner. Also, RBC staining using o‐Dianisidine confirms the anti‐angiogenic potential of BBR by indicating the decrease in the intersegmental vessels at 0.5 and 0.75 mM treated embryos. Further, the gene expression study determined that the transcripts (vegf, vegfr2, nrp1a, hif‐1α, nos2a, nos2b, cox‐2a, and cox‐2b) measured were found to be downregulated by BBR at 0.5 mM concentration, from which we conclude that enos/vegf signaling could play an important role in modulating angiogenesis. Our data imply that BBR may be an effective compound for suppressing angiogenesis in vivo, which might be helpful in the treatment of vascular disorders like cancer and diabetic retinopathy in future.