(1) Background: Whole-body magnetic resonance imaging (WB-MRI) is central to defining total inflammatory burden in juveniles with arthritis. Our aim was to determine and compare the initial distribution of lesions in the WB-MRI in patients with chronic recurrent multifocal osteomyelitis (CRMO), juvenile idiopathic arthritis (JIA), their overlapping syndrome (OS), and with Non-specific Arthropathy (NA). (2) Methods: This retrospective single center study was performed on an Avanto 1.5-T MRI scanner with a dedicated multichannel surface coil system. A total of 173 pediatric patients were included with the following final diagnoses: CRMO (15.0%), JIA (29.5%), OS (4.6%), and NA (50.9%). (3) Results: Bone marrow edema (BME) was the most common abnormality, being seen in 100% patients with CRMO, 88% with OS, 55% with JIA, and 11% with NA. The bones of the lower extremities were the most affected in all compared entities. Effusion was seen in 62.5% children with OS, and in 52.9% with JIA, and in CRMO and NA, the exudate was sporadic. Enthesitis was found in 7.8% of patients with JIA and 3.8% with CRMO, and myositis was seen in 12.5% of patients with OS and in 3.9% with JIA. (4) Conclusions: The most frequent indication for WB-MRI in our center was JIA. The most common pathology in all rheumatic entities was BME, followed by effusion mainly seen in in OS and JIA. Enthesitis and myositis were less common; no case was observed in NA.