Extraintestinal manifestations (EIMs) are observed in 15–20% of patients with inflammatory bowel disease (IBD). One of the rare EIMs is myocarditis, the incidence of which is estimated at around 1%. The main cause of myocarditis is a viral infection. Other causes include autoimmune diseases and drug complications (sulfasalazine, mesalazine). We present the case of an 11-year-old girl with Crohn’s disease (CD) with EIMs, manifested as hip joint inflammation and erythema nodosum. At the same time, the symptoms of myopericarditis appeared with changes in electrocardiogram (ECG), echocardiography and high troponin I concentration. Therapy with corticosteroids resulted in the resolution of skin lesions and cardiological symptoms. Systemic connective tissue diseases, viral and bacterial infections were excluded in the differential diagnosis. The suspicion of mesalazine-induced EIMs was also ruled out as the symptoms resolved despite continued therapy with mesalazine. No further recurrences of myopericarditis were observed.