The purpose of this study was to utilize state-of-the-art on-board digital kilovoltage (kV) imaging to determine the systematic and random set-up errors of an immobilization device designed for canine and feline cranial radiotherapy treatments. The immobilization device is comprised of a custom made support bridge, bite block, vacuum-based foam mold and a modified thermoplastic mask attached to a commercially available head rest designed for human radiotherapy treatments. The immobilization device was indexed to a Varian exact couch-top designed for image guided radiation therapy (IGRT). Daily orthogonal kV images were compared to Eclipse treatment planning digitally reconstructed radiographs (DRRs). The orthogonal kV images and DRRs were directly compared online utilizing the Varian on-board imaging (OBI) system with set-up corrections immediately and remotely transferred to the treatment couch prior to treatment delivery. Off-line review of 124 patient treatments indicates systematic errors consisting of +0.18 mm vertical, +0.39 mm longitudinal and −0.08 mm lateral. The random errors corresponding to 2 standard deviations (95% CI) consist of 4.02 mm vertical, 2.97 mm longitudinal and 2.53 mm lateral and represent conservative CTV to PTV margins if kV OBI is not available. Use of daily kV OBI along with the cranial immobilization device permits reduction of the CTV to PTV margins to approximately 2.0 mm.