Background: Fine-needle aspiration (FNA) coupled with flow cytometry (FC) can be helpful in suspicious pediatric lymph nodes or masses to exclude a lymphoproliferative disorder. The aim of this study was to analyze FC findings in a series of pediatric FNAs and to correlate abnormal findings with follow-up information. Materials and Methods: All pediatric FNAs performed at a tertiary-care children's hospital over a 46-month period that had FC performed were retrospectively analyzed and correlated with follow-up. Results: A total of 163 FNA procedures were performed in children (age ≤21 years), and 47 (28.8%) of these cases had FC performed. Specimens were mostly obtained from the head and neck (72.3% of cases). Nine cases (19.1%) had abnormal FC findings, including double-negative T cells (n = 3; 33.3%), double-positive T cells (n = 3; 33.3%), excess λ light chains (n = 1; 11.1%), weak CD34 positivity (n = 1; 11.1%), and T-lymphoblastic lymphoma (n = 1; 11.1%). Conclusion: Unusual FC results that are not diagnostic of malignancy can be seen in lymph node FNA in a minority of young patients. In our series, these findings were seen mainly in small populations of T cells and occurred primarily in the setting of reactive lymphoid hyperplasia or ectopic thymic tissue. Cytopathologists performing FNA on children should be aware of these abnormalities and, although they may warrant further investigation and follow-up, they are unlikely to be associated with malignancy.