Background: Hematopoietic Stem Cell Transplant (HSCT) is a curative procedure for many life-threatening hematological indications. Respiratory viral infections (RVI) cause substantial morbidity and mortality in pediatric transplant recipients, but the impact of mild/asymptomatic RVI is unclear. Some studies have identified certain viral infections as high-risk for post-transplant complications. To reduce transplant morbidity, a pre-transplant RVI screening program was started at Children’s National Hospital which included symptom screening and respiratory viral (RV) PCR testing for each HSCT patient within one week of and on the day of HSCT admission. The objective of this study was to evaluate the impact of RVI on HSCT outcomes. Methods: A retrospective review of pre-transplant RV PCR, symptom screening, and clinical outcomes was done for patients receiving allogeneic HSCT from 7/1/2016 to 3/31/2023. Exclusion criteria included missing pre-transplant RV PCR and SCID to prevent bias. Results: 161 patients were eligible to be included. Of the 161, 34 tested positive for RVs (26 low-risk, 8 high-risk). Outcomes were initially analyzed separately by low- and high-risk viruses. Within the first 100 days post-transplant, a positive pre-HSCT RVI was significantly associated with increased mortality (odds ratio (OR) = 5.57, p = 0.04 after adjusting for multiple testing) and requirement for ICU transfer (OR = 3.45, p = 0.006). Conclusions: Routine pre-transplant viral testing should be performed to increase the safety of HSCTs. Pre-transplant viral testing may allow providers to know when to monitor certain patients more closely post-transplant, and when to potentially delay elective transplant until the patient has cleared their virus.