This article deals with the experience of the specific client of health services, that is, the patient. Satisfaction questionnaires are usually applied to assess patient experience. However, this tool provides only a cognitive evaluation; it does not afford an affective dimension of the experience. The objective of the present study is to verify the relationship between the cognitive dimension of patient experience, collected through questionnaires, and the affective dimension, derived from the analysis of neurophysiological data. We propose a novel methodology that integrates physiological data collected by facial expression analysis to identify patients’ emotions. A first, qualitative procedure was carried out to define the patient journey. This was recorded on video and later used in the experiment. The experiment collected information from the participants using two techniques. First, as they viewed the videos, facial expression analysis (FEA) was applied to assess their responses. Second, after they watched the videos, traditional questionnaires were presented. The results provided by the two techniques were then compared. The results show that there is no relationship between the emotional valence reported by questionnaires and the neurophysiological data. This reflects the two different dimensions of the experience, one cognitive and the other affective. Both facilitate the understanding of patient satisfaction.