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Objective To apply proposed classification criteria for Periodic Fever, Aphthous stomatitis, Pharyngitis, cervical Adenitis (PFAPA) and Syndrome of Undifferentiated Recurrent Fever (SURF) to a heterogeneous cohort of children with recurrent fever syndromes and evaluate differences in phenotype, treatment response, and disease outcomes. Methods We conducted a retrospective cohort study of 235 children referred to the Autoinflammatory Clinic at The Hospital for Sick Children between 2016 and 2024. Patients were classified as PFAPA or SURF using validated Eurofever/PRINTO classification criteria for PFAPA and empirical indications for SURF. Clinical features, response to corticosteroids, colchicine, and tonsillectomy, time to remission were compared. Phenotypic clusters were identified using principal component analysis (PCA); the log-rank test and Cox proportional hazards regression assessed predictors of remission. Results Of 235 patients, 155 (66%) met PFAPA criteria and 80 (34%) were classified as SURF. PFAPA patients more commonly exhibited classical symptoms (aphthous ulcers, pharyngitis, cervical lymphadenopathy), while SURF was characterized by gastrointestinal and systemic features (abdominal pain, arthralgia, fatigue). Data-driven clustering identified predominant patterns: a classic PFAPA cluster and a gastrointestinal-dominant cluster, underscoring heterogeneity. Neither corticosteroid nor colchicine response was associated with phenotype or remission. Time to remission was shorter in PFAPA than SURF (median 4.8 vs. 5.7 years; p = 0.04). Cox regression confirmed SURF classification as an independent predictor of delayed remission (HR 0.68, p = 0.04). Conclusion Structured classification distinguishes PFAPA and SURF by phenotype and disease trajectory. Data-driven clustering revealed three overlapping phenotypic patterns, supporting a continuum of autoinflammatory expression and emphasizing the need for individualized diagnostic and therapeutic approaches.