When responding to a novel infectious disease outbreak, policies are set under time constraints and uncertainty which can limit the ability to control the outbreak and result in unintended consequences including lack of public confidence. The H1N1 pandemic highlighted challenges in public health decision-making during a public health emergency. Understanding this process to identify barriers and modifiable influences is important to improve the response to future emergencies. The purpose of this study is to examine the H1N1 pandemic decision-making process in Canada with an emphasis on the use of evidence for public health decisions. Using semi-structured key informant interviews conducted after the pandemic (July–November 2010) and a document analysis, we examined four highly debated pandemic policies: use of adjuvanted vaccine by pregnant women, vaccine priority groups and sequencing, school closures and personal protective equipment. Data were analysed for thematic content guided by Lomas' policy decision-making framework as well as indicative coding using iterative methods. We interviewed 40 public health officials and scientific advisors across Canada and reviewed 76 pandemic policy documents. Our analysis revealed that pandemic pre-planning resulted in strong beliefs, which defined the decision-making process. Existing ideological perspectives of evidence strongly influenced how information was used such that the same evidentiary sources were interpreted differently according to the ideological perspective. Participants recognized that current models for public health decision-making failed to make explicit the roles of scientific evidence in relation to contextual factors. Conflict avoidance theory explained policy decisions that went against the prevailing evidence. Clarification of roles and responsibilities within the public health system would reduce duplication and maintain credibility. A more transparent and iterative approach to incorporating evidence into public health decision-making that reflects the realities of the external pressures present during a public health emergency is needed.