A case of exophthalmos due to zygomatic mucocele in a puppy with ipsilateral segmental maxillary atrophy is reported. A 7-month-old, mixed breed, male dog suffered the sudden-onset of unilateral painful exophthalmos and a gradual swelling of the right temporal region. A compressing, right retrobulbar mass was observed by ultrasound. Computed tomography revealed a large multiloculated cyst-like lesion of the right zygomatic gland projecting into the orbital space, thus displacing the eyeball. The ipsilateral molar part of the maxillary bone was underdeveloped, besides showing crowded, abnormal, multiple, unerupted maxillary molar teeth in the caudal maxillary region. Modified lateral orbitotomy and a selective caudal maxillary bone access were performed. The cyst-like lesion was removed and the zygomatic gland and the wall was collected for histology, which confirmed the mucocele. Clinical and imaging examinations six months after surgery showed neither recurrence of the mucocele nor ocular abnormalities. A possible common pathogenic mechanism involving these two conditions could be hypothesized.