The effect of high-intensity thermosonication (HIT) pretreatment (20 kHz frequency, output power 4000 W and 25% amplitude for 5, 10 and 15 min) on the physicochemical and rheological properties of stirred yoghurt made from goat milk was studied. Various parameters of the milk were evaluated, such as the particle size, pH and soluble calcium and phosphorus, while other parameters of the stirred yoghurt were evaluated during storage (up to 18 days), such as the rheological measurements, syneresis, pH values, titratable acidity, color, and sensory properties. The microstructure had more interconnected chains than the stirred yoghurt made from homogenized milk on the first day of the storage period. Moreover, the HIT process reduced the diameter of the fat globules in the goat milk, making them smaller than those of homogenized milk. This pretreatment could be used successfully in the production of stirred yoghurt to improve major quality parameters such as delayed syneresis, increased viscosity and enhanced sensory properties during storage.