Deraniyagala's beaked whale (Mesoplodon hotaula) is one of the least-known beaked whale species, with only a few of possible live sightings being documented to date. Here, vocalizations of Deraniyagala's beaked whales were recorded using drifting recording systems in the confirmed presence of this whale in the northern South China Sea (SCS) in 2021. A total of 699 qualified frequency-modulated (FM) pulses were used to calculate frequency and duration measurements. FM pulses had a median peak frequency of 43.3 kHz and median interpulse interval (IPI) of 244.6 ms. Both the spectra measurements and clustering analysis showed the recorded clicks closely resemble the clicks of beaked whales at Palmyra Atoll (presumed to belong to Deraniyagala's beaked whale). Compared with other Ziphiidae species, interspecific differences were also observed. Distinguishing between Deraniyagala's and ginkgo-toothed (M. ginkgodens) beaked whales with acoustic data sets seems to prove feasible. Our results also suggested that Deraniyagala's beaked whales may produce more than one subtype of FM pulses. This study presents the first description of echolocation clicks produced by this species based on the confirmed visual sightings. It is beneficial to identify the species in passive acoustic monitoring records and gain further insight into this species' vocalizations.