Background: Juvenile idiopathic arthritis (JIA) affecting temporomandibular joints (TMJ) in growing patients results in maxillofacial deformities, especially if only one condyle has been affected by the rheumatic disease. Mandibular hypoplasia is the most common issue and it may be associated with maxillary hypoplasia. The aim of this retrospective case-control study is to evaluate the effects of rapid maxillary expansion (RME) in these patients. Methods: 25 growing patients affected by maxillary hypoplasia, currently in a quiescent phase of JIA for at least one year and monolateral involvement of the TMJs, were treated with RME. Data gathered from posteroanterior and lateral cephalograms before and after 1 year from RME were compared to those of 25 non-JIA controls. Results: Nasal cavity width, maxillary width and upper and lower intermolar width statistically increased. Maxillary and mandibular symmetry indexes presented a statistically significant increase, so did the skeletal class. No signs or symptoms of TMJ activity of JIA occurred according to Research Diagnostic Criteria for Temporomandibular Disorders (RDC/TMD) criteria. No difference was found when comparing JIA and non-JIA patients apart from the better improvement of several mandibular symmetry indexes in the affected TMJ side of JIA patients. This event is allegedly due to a worse baseline asymmetry in JIA patients that underwent a bigger relative improvement after treatment. Conclusions: Results suggest that solving maxillary hypoplasia and, therefore, premature contacts are likely to have allowed mandibular repositioning and condylar growth. RME is a safe and effective solution that can substantially improve maxillary and mandibular symmetry in growing patients affected by JIA with TMJ involvement.