BackgroundMethotrexate (MTX), commonly used in juvenile idiopathic arthritis (JIA), frequently has to be discontinued due to intolerance with anticipatory and associative gastrointestinal adverse effects. Eye Movement Desensitization and Reprocessing (EMDR) is a psychological method where dysfunctional experiences and memories are reprocessed by recall combined with bilateral eye movements. The objective of this study was to assess efficacy of EMDR for treatment of MTX intolerance in JIA patients.MethodsWe performed an open prospective study on consecutive JIA patients with MTX intolerance. Intolerance was determined using the Methotrexate Intolerance Severity Score (MISS) questionnaire prior to treatment, directly after treatment and after four months. Health-related quality of life was determined using the PedsQL prior to and four months after treatment. Patients were treated according to an institutional EMDR protocol with 8 sessions over two weeks. Changes in MISS and PedsQL were analyzed using non-parametric statistics.ResultsEighteen patients with MTX intolerance (median MISS at inclusion 16.5, IQR = 11.75–20.25) were included. Directly after treatment, MTX intolerance symptoms were significantly improved (median MISS 1 (IQR = 0–2). After four months, median MISS score was at 6.5 (IQR = 2.75–12.25, p = 0.001), with 9/18 patients showing MISS scores ≥6.Median PedsQL after 4 months improved significantly from 77.6% to 85.3% (p = 0.008).ConclusionMTX intolerance in children with JIA was effectively treated using an EMDR protocol, with lasting effect over a period of 4 months. EMDR treatment can potentially increase quality of life of affected patients and enable continued MTX treatment.Electronic supplementary materialThe online version of this article (10.1186/s12969-018-0228-y) contains supplementary material, which is available to authorized users.