Objectives: To explore community pharmacies’ experience with two models of distribution for publicly-funded influenza vaccines in Ontario, Canada—one being publicly-managed (2015–2016 influenza season) and one involving private pharmaceutical distributors (2016–2017 season). Methods: Online surveys were distributed to community pharmacies across Ontario during the 2015–2016 and 2016–2017 influenza seasons with sampling proportional to Ontario Public Health Unit catchment populations. Quantitative data were analyzed descriptively and inferentially and qualitative data were summarized for additional context. Results: Order fulfillment appeared more responsive with the addition of private distributors in 2016–2017, as more pharmacies reported shorter order fulfillment times (p < 0.01); however, pharmacies reported significantly more days with zero on-hand inventory in 2016–2017 (p < 0.01), as well as more instances of patients being turned away due to vaccine unavailability (p < 0.05). In both seasons, a similar proportion of pharmacies reported slower order fulfillment and limited order quantities early in the season. Improved availability early in the season when patient demand is highest, more vaccines in a pre-filled syringe format, and better communication from distributors on product availability dates were recommended in qualitative responses. Conclusions: Introducing private distributors for the management and fulfillment of pharmacies’ orders for the publicly funded influenza vaccine appeared to have mixed results. While key concerns surrounding the frequency, responsiveness, and method of delivery were addressed by this change, challenges remain—in particular, acquiring sufficient vaccine early in the season to meet patient demand. As pharmacies become more prominent as vaccination sites, there are several opportunities to ensure that patient demand is met in this setting.