Contamination of water resources by pharmaceutical residues, especially during the time of pandemics, has become a serious problem worldwide and concerns have been raised about the efficient elimination of these compounds from aquatic environments. This study has focused on the development and evaluation of the sonocatalytic activity of a flower-like MoS2/CNTs nanocomposite for the targeted degradation of hydroxychloroquine (HCQ). This nanocomposite was prepared using a facile hydrothermal route and characterized with various analytical methods, including X-ray diffraction and electron microscopy, which results confirmed the successful synthesis of the nanocomposite. Moreover, the results of the Brunauer–Emmett–Teller and diffuse reflectance spectroscopy analyses showed an increase in the specific surface area and a decrease in the band gap energy of the nanocomposite when compared with those of MoS2. Nanocomposites with different component mass ratios were then synthesized, and MoS2/CNTs (10:1) was identified to have the best sonocatalytic activity. The results indicated that 70% of HCQ with the initial concentration of 20 mg/L could be degraded using 0.1 g/L of MoS2/CNTs (10:1) nanocomposite within 120 min of sonocatalysis at the pH of 8.7 (natural pH of the HCQ solution). The dominant reactive species in the sonocatalytic degradation process were identified using various scavengers and the intermediates generated during the process were detected using GC–MS analysis, enabling the development of a likely degradation scheme. In addition, the results of consecutive sonocatalytic cycles confirmed the stability and reusability of this nanocomposite for sonocatalytic applications. Thus, our data introduce MoS2/CNTs nanocomposite as a proficient sonocatalyst for the treatment of pharmaceutical contaminants.