Epstein-Barr virus (EBV) infects the vast majority of the human population. The primary infection in immunocompetent individuals is typically asymptomatic or presenting as infectious mononucleosis. Here, an 18-year-old man without medical history was admitted with mild non-specific symptoms of infection presenting primarily with severe dysphagia and epigastric pain. Gastroscopy revealed severe, extensive, ulcerative oesophagitis with suspicion of Crohn's disease. However, a diagnosis of primary EBV infection presenting as severe ulcerative oesophagitis and without systemic symptoms of infectious mononucleosis was made based on dynamic changes in EBV serology (shift from IgM to IgG positivity), EBV-specific immunohistochemical staining, and PCR analysis of biopsy specimens. This rare manifestation of primary EBV in an immunocompetent patient was treated symptomatically and resolved within a few weeks, and should be considered a differential diagnosis at otherwise unexplained ulcerative oesophagitis in younger individuals.