The PB1-F2 protein of the influenza A viruses (IAV) can act as a virulence factor in mice. Its contribution to the virulence of IAV in swine, however, remains largely unexplored. In this study, we chose two genetically related H3N2 triple reassortant (TR) IAVs to assess the impact of PB1-F2 in viral replication and virulence in pigs. Using reverse genetics, we disrupted the PB1-F2 open reading frame (ORF) of A/swine/WI/14094/1999 (H3N2) [Sw/99] and A/turkey/OH/313053/2004 (H3N2) [Ty/04]. Removing the PB1-F2 ORF led to increase expression of PB1-N40 in a strain-dependent manner. Ablation of the PB1-F2 ORF (or incorporation of the N66S mutation in the PB1-F2 ORF, Sw/99 N66S) affected the replication in porcine alveolar macrophages of only the Sw/99 KO and Sw/99 N66S variants. The Ty/04 KO strain showed decreased virus replication in swine respiratory explants, whereas no such effect was observed in the Sw/99 KO, compared to the WT counterparts. In pigs, PB1-F2 did not affect viral shedding or viral load in the lungs for any of these strains. Upon necropsy, PB1-F2 had no effect on the lung pathology caused by Sw/99 variants. Interestingly, the Ty/04 KO-infected pigs showed significantly increased lung pathology at 3 days post-infection (dpi) compared to pigs infected with the Ty/04 WT strain. In addition, the pulmonary levels of IL-6, IL-8, and IFN-γ were differentially regulated by the expression of PB1-F2. Taken together, these results indicate that PB1-F2 modulates viral replication, virulence, and innate immune responses in pigs in a strain-dependent fashion.