Numerous experimental studies have demonstrated that CD8+ T-cells contribute to immunity against influenza by limiting viral replication. It is therefore surprising that rigorous statistical tests have failed to find evidence of positive selection in the epitopes targeted by CD8+ T-cells. Here we use a novel computational approach to test for selection in CD8+ T-cell epitopes. We define all epitopes in the nucleoprotein (NP) and matrix protein (M1) with experimentally identified human CD8+ T-cell responses, and then compare the evolution of these epitopes in parallel lineages of human and swine influenza that have been diverging since roughly 1918. We find a significant enrichment of substitutions that alter human CD8+ T-cell epitopes in the NP of human versus swine influenza, consistent with the idea that these epitopes are under positive selection. Furthermore, we show that epitope-altering substitutions to human influenza NP are enriched on the trunk versus the branches of the phylogenetic tree, indicating that viruses that acquire these mutations have a selective advantage. However, even in human influenza NP, sites in T-cell epitopes evolve more slowly than non-epitope sites, presumably because these epitopes are under higher inherent functional constraint. Overall, our work demonstrates that there is clear selection from CD8+ T-cells in human influenza NP, and illustrates how comparative analyses of viral lineages from different hosts can identify positive selection that is otherwise obscured by strong functional constraint.