The zebrafish has emerged as an important vertebrate model for genetic screens and new drug development due to its significant characteristics such as optical transparency, rapid ex vivo growth, and high genetic similarity to humans. Despite these benefits, the scale of zebrafish studies is still limited as a result of the lack of a robust method to manipulate zebrafish during screening. In this work a new microfluidic channel layout in conjunction with a series of magnetically actuated artificial cilia were employed to provide orientation control of zebrafish larvae with axial rotation capability. This method enables 0-15 degrees of rotation inside the microchannel with high accuracy and less detrimental impact, as opposed to the conventional methods. In addition, the bioactivity of tested larvas remains stable with no significant difference to those in the control group during the time-lapse imaging. The presented platform along with the provided analytical paradigm is forecasted to be beneficial to facilitate the zebrafish screening using microfluidics in pharmaceutical industry.