A three-dimensional in vivo near-infrared photoacoustic tomography imaging system was newly designed and built to visualize the structure of a whole small animal head. For high sensitivity, a single flat 2.25MHz low frequency transducer, whose active element size is 6mm, was employed. To increase the penetration depth of light, a wavelength of 804nm in the NIR range, which matches the oxy- and deoxy-hemoglobin isosbestic point, was chosen. To avoid strong photoacoustic signal generation from the skin surface, we applied dark field illumination. To illuminate efficiently, we split the laser light into two beams, which were delivered to an animal by two mirrors and were finally homogenized by two ground glasses. To complete the dark field illumination, the transducer was located in the middle of two light sources. Two key devices for the in vivo imaging were rotating devices and animal holders. The rotating devices were composed of two parts, located at the top and bottom, which rotated at the same angular speed. The holders were composed of a head holder and a body holder. Both holders fixed the animal firmly to reduce motion artifacts. This system achieved radial resolution of up to 260μm. We accomplished successful in vivo imaging of arterial and venous vessels deeply, as well as superficially, with the animal head of up to 1.7cm diameter. The technique forms a basis for functional imaging, such as measurement of the oxygen consumption ratio in the brain, which is a vital parameter in a brain disease research.