Variable prevalence and treatment of breakthrough pain (BTP) in different clinical contexts are partially due to the lack of reliable/validated diagnostic tools with prognostic capability. We report the statistical basis and performance analysis of a novel BTP scoring system based on the naïve Bayes classifier (NBC) approach and an 11-item IQ-BTP validated questionnaire. This system aims at classifying potential BTP presence in three likelihood classes: “High,” “Intermediate,” and “Low.”