Abstract Background Persistent, unpredictable pain is one of the most burdensome features of juvenile idiopathic arthritis (JIA) which is a relapsing-remitting inflammatory musculoskeletal condition presenting in children and young people under 16 years. Recent research into perceptions of illness in young people has found that conceptualisations of long-term disease are mainly about the most salient features and symptoms, not of the illness as a whole. Particularly in young people with JIA, perceptions of pain are central to the individuals’ beliefs about the chronic condition. In paediatric pain research in general, the study of pain beliefs has mainly focused on pain catastrophising. Associations between other potentially important pain beliefs and pain outcomes (e.g. reporting pain or well-being) have not been explored to date. The aim of this study was to explore a wide range of pain perceptions in young people with JIA and to investigate whether these pain beliefs were associated with pain severity or well-being. Methods Cross-sectional data from the largest UK cohort study of children with JIA were analysed (the Childhood Arthritis Prospective Study- CAPS). Participants aged over 11 years completed ‘The Pain Perceptions Questionnaire for Young People (PPQ–YP)’ which assesses pain beliefs corresponding to the Common Sense-Self Regulatory framework first proposed by Leventhal and colleagues in the 1980s. Self-reported pain severity scores were captured using a Visual Analogue Scale (VAS). Emotional well-being was assessed using the Positive and Negative Affect Scale (PANAS). Associations were explored using Spearman’s Rank Correlation. Results 223 participants (64% female) completed the PPQ-YP. 38.2% of participants had a diagnosis of oligoarthritis, 29.6% had polyarthritis and equal proportions of participants had systemic, psoriatic or enthesitis related JIA (7.3%). Higher reported pain severity was significantly correlated with stronger beliefs about the greater impact of pain on life (rho=0.494, p < 0.001), pain unpredictability (rho=0.369, p < 0.001) and pain persistence (rho=0.278,p<0.001). Higher pain controllability beliefs (that pain was controllable) were significantly associated with lower self-reported pain severity (rho=-0.526, p < 0.001). Stronger beliefs about the impact of pain on life (rho=0.425,p=0.001) and pain coherence (poorer understanding about own pain: rho=-0.295,p=0.021) were significantly associated with more negative mood. Conclusion Pain beliefs (particularly about consequences, unpredictability, persistence and understanding) are linked to levels of pain severity and well-being in children with JIA. Adding to the evidence base on the link between pain catastrophising and illness outcomes, this research enhances our understanding of long-term illness and pain perceptions in young people through the implication of a wider range of pain beliefs and cognitions on illness outcomes. The PPQ-YP identified salient pain beliefs which should be considered in the design of potential interventions to improve pain outcomes in this group. Future research should aim to explore whether these perceptions can predict other important illness outcomes. Conflicts of Interest The authors declare no conflicts of interest.