Mass immunization clinics (MICs) are an important component of pandemic influenza control strategies in many jurisdictions. Decisions about staffing levels at MICs affect several factors of concern to public health authorities: total vaccination volume, patient wait-times, operating costs, and intra-facility influenza transmission risk. We present a discrete-event simulation of an MIC to assess how strongly staffing changes affect these factors. The simulation is based on data from Canadian clinics responding to pandemic H1N1 in 2009. This study is the first to model flu transmission risk at an MIC, and the first to relate such risk to staffing decisions. We show that the marginal benefit of adding staff is greatly underestimated if indirect waiting costs and intra-facility infections are not considered.