One of the most prevalent diseases in humans is musculoskeletal dysfunction. The source of these problems is usually multifactorial, including mechanical, psychological, and chemical. A specific diagnosis is rarely achieved for most musculoskeletal disorders, especially chronic conditions. This can be one of the reasons for the ineffectiveness of the various treatments offered. Various models have been proposed to address this problem to make more accurate diagnoses and effective treatments. Each of these models has its limitations. It seems that the previous models had limited information, such as the type of damaged tissue, the stage of tissue repair, the functional aspect of the disorder, other parts of the movement chain disorder, psychological features, and a lack of correlation between medical diagnosis and physiotherapy diagnosis. In the present study, an attempt is made to provide a new and more comprehensive model by considering the limitations of other models. In the first step, the therapist or physician identifies the biomechanical source of the disorder. The patient’s functional movement impairments are identified, and a Neuro-Musculo-Skeletal disorder related to functional movement impairment is assessed. Finally, to label the patient’s problem, medical (Patho-Anatomical Model) and physical therapy (Movement System Classification Models) views are considered. Therefore, the medical diagnosis of the patient is expressed along with the joints that play a role in aggravating the patient’s symptoms with movement. One case study is provided at the end to clarify the method of diagnosis. Future research is necessary to improve the validity of the methodology.