Assuming a symmetric pattern plays a fundamental role in the diagnosis and surgical treatment of facial asymmetry, for reconstructive craniofacial surgery, knowing the precise location of the facial midline is important since for most reconstructive procedures the intact side of the face serves as a template for the malformed side. However, the location of the midline is still a subjective procedure, despite its importance. This study aimed to automatically locate the bilateral symmetry midline of the facial skeleton based on an invariant moment technique using pseudo-Zernike moments. A total of 367 skull images were evaluated using the proposed technique. The technique was found to be reliable and provided good accuracy in the symmetry planes. This new technique will be utilized for subsequent studies to evaluate diverse craniofacial reconstruction techniques.