During pandemic influenza, several factors could significantly impact the outcome of vaccination campaigns, including the delay in pandemic vaccine availability, inadequate protective efficacy, and insufficient number of vaccines to cover the entire population. Here, we incorporate these factors into a vaccination model to investigate and compare the effectiveness of the single-dose and two-dose vaccine strategies. The results show that, if vaccination starts early enough after the onset of the outbreak, a two-dose strategy can lead to a greater reduction in the total number of infections. This, however, requires the second dose of vaccine to confer a substantially higher protection compared to that induced by the first dose. For a sufficiently long delay in start of vaccination, the single-dose strategy outperforms the two-dose vaccination program regardless of its protection efficacy. The findings suggest that the population-wide benefits of a single-dose strategy could in general be greater than the two-dose vaccination program, in particular when the second dose offers marginal increase in the protection induced by the first dose.