Despite the temporomandibular joint (TMJ) being a well-known anatomical structure its diagnosis may become difficult because physiological sounds accompanying joint movement can falsely indicate pathological symptoms. One example of such a situation is temporomandibular joint hypermobility (TMJH), which still requires comprehensive study. The commonly used official research diagnostic criteria for temporomandibular disorders (RDC/TMD) does not support the recognition of TMJH. Therefore, in this paper the authors propose a novel diagnostic method of TMJH based on the digital time–frequency analysis of sounds generated by TMJ. Forty-seven volunteers were diagnosed using the RDC/TMD questionnaire and auscultated with the Littmann 3200 electronic stethoscope on both sides of the head simultaneously. Recorded TMJ sounds were transferred to the computer via Bluetooth® for numerical analysis. The representation of the signals in the time–frequency domain was computed with the use of the Python Numpy and Matplotlib libraries and short-time Fourier transform. The research reveals characteristic time–frequency features in acoustic signals which can be used to detect TMJH. It is also proved that TMJH is a rare disorder; however, its prevalence at the level of around 4% is still significant.