The influenza vaccine is critical for preventing influenza‐related complications in transplant patients. Previous studies demonstrated de novo donor‐specific antibody formation and rejection following the influenza vaccination. This risk has not been adequately assessed in the pediatric population. We performed a single‐center retrospective analysis of 187 unique pediatric kidney transplant recipients, transplanted from January 1, 2006, to December 31, 2015, assessing for an association of the influenza vaccination with various transplant outcomes. The influenza vaccine was received by 125 of 187 patients within the first year post‐transplant. Using log‐rank tests and Kaplan‐Meier curves, vaccinated patients had a significantly lower risk of mortality (P = 0.048). There were no differences in death‐censored graft survival (P = 0.253), graft survival (P = 0.098), or rejection (P = 0.195) between vaccinated and unvaccinated groups. To address the problem of multiple exposures for a yearly vaccine, Cox proportional hazards regression was utilized with post‐transplant vaccination status considered as a time‐dependent covariate; analyses were performed using both a 360‐ and 180‐day vaccination period following any post‐transplant influenza vaccination. In this model, being vaccinated did not result in a significant difference in mortality (HR 0.90 [0.16, 5.15], P = 0.91), death‐censored graft survival (HR 0.70 [0.31, 1.58], P = 0.39), graft survival (HR 0.69 [0.32, 1.49], P = 0.34), or rejection (HR 0.67 [0.37, 1.19], P = 0.17). Eight patients developed de novo donor‐specific antibodies following the first post‐transplant influenza vaccination; three then developed biopsy‐proven rejection. These results suggest influenza vaccination is safe in pediatric kidney transplant recipients, and larger prospective studies are required to conclusively confirm our findings.