Pain is undesirable, whether it is a symptom of mild or severe illness or instead indicates disorder in the nervous system’s ability to perceive and process sensory information. Nonetheless, pain is part of the body’s ability to defend itself and promote its own survival—this is its fundamental evolutionary function. This normal expression of pain is not limited to what is considered useful because it alerts us to the initiation of illness. It also applies to pain that continues when illness or noxious stimuli persist. However, the parameters of what is here termed functional pain are not fully understood and are seldom explicitly the focus of research. This paper posits that failure to appreciate the functional role of pain in research has had significant unintended consequences and may be contributing to inconsistent research findings. To that end, the paper describes the misclassification issue at the core of chronic pain research—whether a given pain reflects functional or pathological processes—and discusses research areas where reconsidering the functional role of pain may lead to advancements.