Objective The aim of this study is to assess the diagnostic value of magnetic resonance imaging (MRI) in children with acute lymphoblastic leukemia (ALL) misdiagnosed as juvenile idiopathic arthritis (JIA). Methods Retrospective analysis was performed on children with lower extremity pains as the first symptom in our hospital from January 2018 to December 2020 who were initially diagnosed as JIA. Among them, fifteen patients were finally diagnosed as ALL confirmed by bone marrow aspiration, eighteen patients were JIA. All of them underwent blood routine and bilateral knee MRI examination before any treatment. The MRI were performed, including T1WI, spectral attenuated inversion recovery (SPAIR) T2WI and DWI (b value was 0 and 600 s/mm²). The MRI features of bone marrow were assessed by extent and location, the signal intensity, morphological features. The ADC value of all knee joints were measured and were compared between the two groups. The diagnostic value was calculated. Results There were no statistically significant differences in WBC count, hemoglobin (Hb), platelet count (PLT), C- creative protein (CRP) and erythrocyte sedimentation rate (ESR) between the case group and the control group (P>0.05). Abnormal signal intensity of bone marrow in bilateral bones of lower extremities was demonstrated in 13 patients with ALL patients which showed diffuse homogeneous iso- or low-signal intensity on T1W images and high signal intensity on T2 SPAIR images; other 2 patients had normal results of MRI. In 18 patients with JIA, 14 patients showed ill-defined patchy areas in the metaphysis and epiphysis with iso- or low-signal intensity on T1W images and high signal intensity on T2 SPAIR images; other 4 cases of JIA patients had normal results of MRI. The positive rate in the case group was higher than that in the control group. Compared with the control group, the MRI features of the case group were bilateral diffuse low signal intensity in T1W images and high signal intensity in T2W images (P<0.01). The ADC values in ALL group were lower than control group (t=-14.133, P<0.01). Taking 0.88×10^-3 mm² /s as the threshold, AUC of ROC curve in diagnosis of ALL was 0.895, with sensitivity, specificity and diagnostic accuracy was 86.7%, 83.3% and 84.9%. Conclusion MRI may serve as a noninvasive method to help discrimination of ALL from JIA in children presenting with lower extremity pains. MRI show diffuse abnormal signal intensity on bilateral lower extremities are more likely to be initial ALL.