Findings are reported from an evaluation of the performance of the 2013 Canterbury under-18 Seasonal Influenza Vaccination Programme (Christchurch, NZ). Overall uptake of influenza vaccination in 2013 was 32.9% (increased from 18.5% in 2012), close to the target of 40%. Overall uptake in primary care was higher than in the school-based programme (29.2% vs 19.7%). Māori students had higher uptake than NZ European students in the school-based programme. In primary care, uptake for both Māori and Pacific children was lower than overall uptake and there was a marked gradient in uptake by socioeconomic quintile, with 30.2% uptake in the least deprived quintile (richer areas) compared to 21.9% uptake in the most deprived quintile (poorer areas). Qualitative analysis of interviews held with participating schools identified that the health and education sectors need to improve partnership and communication, to improve vaccination uptake still further.