We present a case of a nine-year-old girl with Crohn’s disease whose only first manifestation was fever. The patient was treated with antibiotics for six weeks by her general practitioner via teleconsultations during the COVID-19 pandemic. However, no significant improvement was observed. Only the appearance of loose stools after six weeks of observation and the lack of effect of previous treatment allowed for targeting of the diagnostic process and an unequivocal recognition of Crohn’s disease. Our aim is to emphasize the difficulties in diagnosis related to the atypical course of the disease, especially in the context of the ongoing COVID-19 pandemic. The described course of Crohn’s disease occurs in a minority of patients; however, this disease should not be overlooked in the differential diagnosis of fever in paediatric patients.