Injection and extraction of materials (e.g. protein, sperms, DNA, and blastomeres) into and from cells are essential operation for In Vitro Fertilisation (IVF), intracytoplasmic sperm injection (ICSI) and preimplantation genetic diagnosis (PGD). In order to perform the injection and extraction without damage to the cell, the cell needs to be at an optimal orientation. In this paper, a fully automated microrobotic system for cell orientation is presented. The proposed system overcomes several inherent problems in manual cell manipulation, including low efficiency, inconsistent output and poor success rate. The system can rotate a single fish embryo to a desired orientation by employing motion control, fluidic flow control, and computer vision. It is evaluated by using 60 Zebrafish embryos. Experimental results show that the system is capable of performing fast embryo orientation at a speed of 13 s/cell with a high success rate of 97.5% and a high in-plane rotation precision of 0.5°.