This study developed a high frequency ultrasound computed tomography (UCT) imaging system for small animal imaging. Both attenuation and sound velocity UCT were used to recognize the tissue properties with a high image contrast. The center frequencies of transducers ranging from 25 to 40 MHz were used in this system. The high frequency transducer was mounted on a three axes step motor system for linear scan, and the object was fixed on a rotational stage which was controlled by another step motor. The projections of object at different angles were obtained by measuring the sound speed and relative attenuation passed through the object. The filtered backprojection algorithm was used to reconstruct the two dimensional UCT image. The resolution of the system was verified by scanning a 200 μm diameter micro-tube. The system verification was performed by imaging the gelatin phantoms and zebrafish. In phantom experiments, the phantom was composed of two different gelatins (gelatin concentration for 4% and 6%). In contrast to ultrasound B-mode image, the slight difference in different concentration gelatins can be recognized easily by using the UCT system. For small animal experiments, most organs of zebrafish can be observed by high frequency UCT images. All the results indicate that the UCT has great potential applications in imaging small animal, such as zebrafish liver tumor and rat testicle.