Background Juvenile idiopathic arthritis (JIA) is a chronic autoinflammatory disease of unknown etiology and is the most common cause of autoimmune musculoskeletal disease in children. Pain is a commonly reported symptom in JIA. There are levels of pain that interfere with physical, educational, emotional, and social activity, even when disease activity is controlled. Assessment of pain at each office visit is the cornerstone of effective pain management. Pediatric Pain Questionnaire (PPQ) uses a 100-mm horizontal visual analog score (VAS) anchored with happy and sad faces to assess the present pain intensity and the worst pain intensity in the past week. Patients are also asked to choose from a list of 46 word descriptors to express sensory (e.g., cutting), affective (e.g., horrible), and evaluative (e.g., sad) qualities of their pain. Aim The aim of the study was to assess pain in children with JIA attending the Rheumatology Clinic in Alexandria University Children’s Hospital and to determine its relation to disease activity. Patients and methods Fifty-eight patients and their parents who attended the Pediatric Rheumatology Clinic of Alexandria University Children Hospital were asked to fill out the questionnaire. Of the patients 58.6% were females and 41.4% patients were males; the mean age of the patients was 10.36±3.34 (months). Results According to pain and emotion, most parents in this study answered that the pain seemed worse when their children are tired. Distribution of the studied cases for present pain on VAS in this study showed that no significant differences were found between the children and parent scorings of present pain on VAS. All correlations were highly significant for present pain (P<0.001*). The distribution of the studied cases for worst pain last week on the VAS showed no significant differences between the children and parents scorings of worst pain on the VAS. All correlations were highly significant for worst pain (P<0.001*). Distribution of the studied cases according to the relationship between pain intensity on VAS and disease activity score showed no significant difference between pain intensity reported by children, parents, and physicians on VAS and disease activity score. Conclusion This work should be viewed in the light of some potential limitations. The results of this study revealed that the PPQ questionnaire was valid, reliable, and sensitive to the assessment of pain. Integrating patient-reported outcome measures of pain severity and responsiveness to standard clinical practice is feasible and applicable in the follow-up of patients and monitoring the treatment effectiveness.