Physiological functions of vascular endothelial cells (ECs) vary depending on wall shear stress (WSS) magnitude, and the functional change affects the pathologies of various cardiovascular systems. Several in vitro and in vivo models have been used to investigate the functions of ECs under different WSS conditions. However, these models have technical limitations in precisely mimicking the physiological environments of ECs and monitoring temporal variations of ECs in detail. Although zebrafish (Danio rerio) has several strategies to overcome these technical limitations, zebrafish cannot be used as a perfect animal model because applying various WSS conditions on blood vessels of zebrafish is difficult. This study proposes a new zebrafish model in which various WSS can be applied to the caudal vein. The WSS magnitude is controlled by blocking some parts of blood-vessel networks. The accuracy and reproducibility of the proposed method are validated using an equivalent circuit model of blood vessels in zebrafish. The proposed method is applied to lipopolysaccharide (LPS)-stimulated zebrafish as a typical application. The proposed zebrafish model can be used as an in vivo animal model to investigate the relationship between WSS and EC physiology or WSS-induced cardiovascular diseases.