We present the design, setup and results for a magnetic navigation system for small animal stereotactic neurosurgery. Our system tracks the position of thin (diameter 0.5 mm), magnetized ferromagnetic probes inserted into brains of small animals, e.g. rats, for electrophysiological recordings. It is used in combination with the spherical assistant for stereotactic surgery (SASSU) robot to obtain online feedback of the probe's position. Navigation is based only on the static magnetic field generated by the probes thus no external excitation or wires are needed.