Abstract Background The impact of Epstein–Barr virus (EBV) infection on the clinical outcomes of children and adolescents with inflammatory bowel disease (IBD) is not well known. The aim of the study is to evaluate the seroprevalence, seroconversion rate and complications associated with EBV infection in a cohort of paediatric IBD (PIBD) patients at a tertiary care hospital. Methods A descriptive study was performed collecting demographic, clinical and treatment data from medical records as well as EBV serological status of paediatric IBD patients from 2012 to 2018. In seronegative patients, seroconversion rate was evaluated. Complications associated with primary EBV infection were described. Since September 2016, EBV serology was included into the initial work-up for PIBD patients. For those patients who did not have EBV study at IBD onset, it was performed during follow-up. Results A total of 307 patients with PIBD were diagnosed between 2012 and 2018. EBV status was available for 131 patients (43%). Of those, 57% had Crohn’s Disease, 41% Ulcerative Colitis, and 2% IBD unclassified (66% males; median age at IBD diagnosis: 13.2 years (IQR: 0.8–17.8)). In 102 patients serological EBV status was determined at IBD onset; while in 17 patients it was performed during the follow-up. Overall, EBV seroprevalence was 67%, and no differences were observed regarding age (over or under 10 years-old). EBV seroprevalence was higher in females than in males (80% vs. 60.5%, p = 0.02). Regarding IBD treatment, 84% had received immunosuppressive treatment [thiopurines (32%), anti-TNF (9%) and combined treatment (59%)], without differences in the seroprevalence rate according to the treatment modality. Forty-three patients were seronegative, and 12 of them had a second determination during follow-up. Overall, 5 patients showed seroconversion (42%) after a mean follow-up of 24 months (IQR: 22–26). All these patients had received treatment with thiopurines: 2 patients presented symptomatic mononucleosis with neutropenia, requiring hospital admission and withdrawal of immunosuppressive treatment and 3 patients had asymptomatic primary infection. Conclusion EBV seroprevalence in our paediatric IBD cohort is similar as previously described in the literature. EBV status study in patients with IBD, especially prior to initiation of thiopurines, may be useful to plan subsequent follow-up since a non-negligible percentage of them could present with complicactions of primary EBV infection under immunosuppressive treatment.