Allogeneic hematopoietic stem cell transplantation (HSCT) is the treatment of choice for many high-risk pediatric hematological malignant diseases (MD) and several nonmalignant diseases (NMD), including primary immune deficiencies. Infections must be managed to obtain better outcomes after HSCT. In this prospective observational study, viral monitoring was performed on 74 pediatric patients with MD and NMD who underwent HSCT. The incidence, risk factors, and impact of common opportunistic viral infections occurring within the first 100 days following HSCT were assessed. The viral pathogens included human herpesviruses, BK polyomavirus (BKV), adenovirus, parvovirus B19, and hepatitis B virus. In total, 52 (70%) patients had viral DNAemia, and 53% and 41% of patients developed human herpesvirus 6 (HHV-6) and cytomegalovirus (CMV) DNAemia, respectively. The risk factors were as follows: negative CMV serology for any viral infections; age ≥ 2 years and negative CMV serology for HHV-6; age ≥5 years and female sex for BKV. The risk of viral infection did not significantly differ between MD and NMD, and no risk factor was identified for viral disease, likely because of the small sample numbers. However, despite the absence of symptoms, CMV DNAemia was found to increase the risk of mortality. The findings of the current study could improve the risk stratification and the management of pediatric HSCT recipients.