Measurement of thyroid size and volume is a useful clinical parameter in both human and veterinary medicine, particularly for diagnosing thyroid diseases and guiding corrective therapy. Procuring a fully-equipped clinical ultrasound unit (FCUS) may be difficult in most veterinary settings. The present study evaluated the inter-equipment variability in dolphin thyroid ultrasound measurements between a portable ultrasound unit (PUS) and a FCUS; for both units, repeatability was also assessed. Thyroid ultrasound examinations were performed on 15 apparently healthy bottlenose dolphins with both PUS and FCUS under identical scanning conditions. There was a high level of agreement between the two ultrasound units in dolphin thyroid measurements (ICC = 0.859–0.976). A high intra-operator repeatability in thyroid measurements was found (PUS: ICC = 0.854–0.984, FCUS: ICC = 0.709–0.954). As a conclusion, no substantial inter-equipment variability was found between PUS and FCUS in dolphin thyroid size measurements under identical scanning conditions, supporting further application of PUS for quantitative analyses of dolphin thyroid gland in both research and clinical practices at aquarium settings.