Topical consumer interest in natural, healthier, safer and nutritional juice, has inspired the search for innovative technologies that can minimize product degradation. In this regard, thermosonication has been proposed as a potential processing technology that can preserve and produce “fresh” products. Watermelon (Citrulluslanatus) juice is a nutrient-rich fruit juice that is desired by consumers due to its appealing color, pleasant odor, sweet taste and low-calorie content. This fruit juice is, however, highly perishable and prone to microorganisms, because of its neutral pH value and high amount of water activity. In addition, it is thermo-sensitive and therefore degrades quickly under thermal processing. This study aimed to identify the optimal thermosonication processing conditions for retaining the critical quality parameters (lycopene, β-carotene, ascorbic acid and total polyphenolic content) of watermelon juice. Response surface methodology, employing a central composite design, was used to determine the effects of temperature (18–52 °C), processing time (2–13 min) and amplitude level (24–73 μm) at a constant frequency of 25 kHz. The highest quality parameters were obtained at 25 °C, 2 min, and 24 µm at a constant frequency of 25 kHz, which resulted in lycopene of 8.10 mg/100 g, β-carotene of 0.19 mg/100 g, ascorbic acid of 3.11 mg/100 g and total polyphenolic content of 23.96 mg/GAE/g with a desirability of 0.81. The proposed model was adequate (p < 0.0001), with a satisfactory determination coefficient (R2) of less than 0.8 for all phytochemicals. Thermosonicated watermelon juice samples showed minimal changes in their phytochemical properties, when compared to fresh juices; the lycopene content showed a significant increase after thermosonication, and a significant retention of β-carotene, ascorbic acid and total polyphenolic acid was observed. According to the findings, thermosonication could be a viable method for preserving watermelon juice, with minimal quality loss and improved functional attributes.