Aim: The aim of the study was to analyze the efficiency when planning complex oral rehabilitation, conducting proper preparation, occlusal analysis and adjustment during the stages of orthodontic treatment in young patients with Juvenile Idiopathic Arthritis. Materials and Methods: 11 young patients with diagnosis of Juvenile Idiopathic Arthritis (according to ILAR criteria) aged from 18 to 34 years (mean age 22.64±4.82) who included 6 females and 5 males were examined and underwent orthodontic treatment at Dental Medical Center of Bogomolets National Medical University during 2021-2024 years. The orthodontic treatment was carried out after oral cavity sanation and elimination of temporomandibular disorders manifestations using occlusal splints and was combined with local medication therapy (mouth rinse using medicinal composition of highly dispersed silica gel and bacteria strains of Bacillus subtilis B-7812(АХ20) and Bacillus licheniformis IMB B-7811(EA22)). Occlusal analysis and adjustments were carried out during all stages of rehabilitation. Results: Provided orthodontic treatment in combination with application of bite blocks and direct dental hard tissues restorations allowed to expand the dental arches, align the midline and normalize the occlusal contacts of the teeth in static and dynamic occlusion in all patients. There were no signs of premature contacts, occlusal overload, deterioration of periodontal lesion or temporomandibular disorder manifestation recurrence. Conclusions: Our study showed that the proposed complex rehabilitation of patients with JIA including proper occlusal analysis and adjustment and probiotics usage during orthodontic treatment within the framework of a personalized approach during their rehabilitation ensures minimization of risks and is the key to achieving optimal results.