Background: The 2009 H1N1 vaccination campaign was the largest in US history. State health departments received vaccines from the federal government and sent them to local health departments (LHDs) who were responsible for getting vaccines to the public. Many LHD's used school-based clinics to ensure children were the first to receive limited vaccine supplies, but the success of school-based distribution strategies varied in different locations. The goal of this project was to identify and learn from high-performing school-based vaccination clinics in order to share successes and improve performance in future school-based vaccination campaigns. Methods: We used a combination of process mapping and comparative analysis to identify and derive lessons from positive outlier cases observed during 2009 H1N1 school-based vaccination clinic implementation. We created process maps to identify the activities of LHDs conducting school-based vaccinations and used them as the basis for in-depth interviews of LHD staff. We asked interviewees to describe their activities during the 2009 H1N1 pandemic (pH1N1) school-based vaccination campaign with a focus on successful processes. Results: We identified positive deviants, that is, those that performed better than expected, and categorized qualitative data from in-depth interviews with 13 successful LHDs according to the process maps. Key mechanisms for school-based vaccination success included having a relationship with local school authorities, communicating effectively with parents, and ensuring clinic logistics allowed for an easy flow of students through the vaccination process. Conclusions: Utilizing rigorous methodology, we defined and learned lessons from successful LHDs when conducting school-based vaccination clinics, which can be applied to future school-based vaccination campaigns.