Background/Objectives: Seasonal influenza annually puts a significant burden on the pediatric population, especially the youngest, causing severe illness and death. Additionally, associated healthcare costs cause a significant financial strain on healthcare systems. While vaccination is the most effective prevention method, its cost-effectiveness for healthy children remains unassessed. Methods: Using the Pedianet database spanning from 2009 to 2019, we analyzed influenza cases among 6-month-olds to 14-year-olds in Italy. Data included influenza-related medical visits, prescriptions, exams, emergency visits, hospitalizations, and costs. Adverse events and quality-adjusted life years (QALYs) were considered from the existing literature. A static decision-tree model compared annual vaccination strategies, assessing probabilities for influenza or influenza-like illnesses by vaccination status. Incremental cost-effectiveness ratios (ICERs) were calculated, along with sensitivity analyses and cost-effectiveness acceptability curve generation. Results: Mean total influenza costs for vaccinated children averaged EUR 18.6 (range 0–3175.9, including EUR 15.79 for the influenza vaccination), whereas costs for unvaccinated children were consistently lower at around EUR 4.6 (range 0–3250.1). The average ICER for years where vaccine and virus strains are matched was EUR 29,831 per QALY, which is below the EUR 40,000 threshold set by the Italian National Health Services. The ICER values range from EUR 13,736 (2017/2018) to EUR 72,153 (2013/2014). Averted influenza costs averaged EUR 23 per case, with fluctuations over the years. In most observed years, influenza vaccination was cost-effective from the healthcare providers’ standpoint. The exception was 2009–2010, due to a mismatch between vaccine and virus strains. Conclusions: This study highlights the economic viability of influenza vaccination, especially when virus and vaccine strains align. It demonstrates the potential of vaccination programs in preserving children’s health and well-being while managing healthcare costs.