Dysfunctional breathing (DB) is a disabling condition which affects the biomechanical breathing pattern and is challenging to diagnose. It affects individuals in many circumstances, including those without underlying disease who may even be athletic in nature. DB can also aggravate the symptoms of those with established heart or lung conditions. However, it is treatable and individuals have much to gain if it is recognized appropriately. Here we consider the role of cardiopulmonary exercise testing (CPET) in the identification and management of DB. Specifically, we have described the diagnostic criteria and presenting symptoms. We explored the physiology and pathophysiology of DB and physiological consequences in the context of exercise. We have provided examples of its interplay with co-morbidity in other chronic diseases such as asthma, pulmonary hypertension and left heart disease. We have discussed the problems with the current methods of diagnosis and proposed how CPET could improve this. We have provided guidance on how CPET can be used for diagnosis, including consideration of pattern recognition and use of specific data panels. We have considered categorization, e.g., predominant breathing pattern disorder or acute or chronic hyperventilation. We have explored the distinction from gas exchange or ventilation/perfusion abnormalities and described other potential pitfalls, such as false positives and periodic breathing. We have also illustrated an example of a clinical pathway utilizing CPET in the diagnosis and treatment of individuals with suspected DB.