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Background: In 2013 England and Wales began to fund a live attenuated influenza vaccine programme for individuals aged 2–16 years. Mathematical modelling predicts substantial beneficial herd effects for the entire population as a result of reduced influenza transmission. With a decreased influenza-associated disease burden, existing immunisation programmes might be less cost-effective. The aim of this study was to assess the epidemiological effect and cost-effectiveness of the existing elderly and risk group vaccination programme under the new policy of mass paediatric vaccination in England. Methods: For this cost-effectiveness analysis, we used a transmission model of seasonal influenza calibrated to 14 seasons of weekly consultation and virology data in England and Wales. We combined this model with an economic evaluation to calculate the incremental cost-effectiveness ratios, measured in cost per quality-adjusted life-years (QALY) gained. Findings: Our results suggest that well timed administration of paediatric vaccination would reduce the number of low-risk elderly influenza cases to a greater extent than would vaccination of the low-risk elderly themselves if the elderly uptake is achieved more slowly. Although high-risk vaccination remains cost-effective, substantial uncertainty exists as to whether low-risk elderly vaccination remains cost-effective, driven by the choice of cost-effectiveness threshold. Under base case assumptions and a cost-effectiveness threshold of £15 000 per QALY, the low-risk elderly seasonal vaccination programme will cease to be cost-effective with a mean incremental cost-effectiveness ratio of £22 000 per QALY and a probability of cost-effectiveness of 20%. However, under a £30 000 per QALY threshold, the programme will remain cost-effective with 83% probability. Interpretation: With the likely move to decreased cost-effectiveness thresholds, reassessment of existing risk group-based vaccine programme cost-effectiveness in the presence of the paediatric vaccination programme is needed. Funding: National Institute for Health Research, the Medical Research Council.