Potential of modern thermal imaging for screening and differentiation of joint inflammation has not been assessed in child and juvenile patient populations, typically demanding groups in diagnostics of musculoskeletal disorders. We hypothesize that thermal imaging can detect joint inflammation in patients with juvenile idiopathic arthritis or autoimmune disease with arthritis such as systemic lupus erythematosus. To evaluate the hypothesis, we studied 58 children exhibiting symptoms of joint inflammation. First, the patients' joints were examined along clinical procedure supplemented with ultrasound imaging when deemed necessary by the clinician. Second, thermal images were acquired from patients' knees and ankles. Results of thermal imaging were compared to clinical evaluations in knee and ankle. The temperatures were significantly (pmax = 0.044, pmean < 0.001) higher in inflamed ankle joints, but not in inflamed knee joints. No significant difference was found between the skin surface temperatures of medial and lateral aspects of ankle joints. In knee joints the mean temperatures of medial and lateral aspect differed significantly (p = 0.004). We have demonstrated that thermal imaging may have potential for detecting joint inflammation in ankle joints of children. For knee joints our results are inconclusive and further research is warranted.