In this study, we investigated the regulation of lncRNA MALAT1 expression and its role during the influenza A virus (IAV) infection. We found that IAV infection robustly upregulated the expression of MALAT1 in vitro and in vivo. Furthermore, we demonstrated that MALAT1 expression was regulated via the NF-κB/IL-6/STAT3 pathway in host cells infected with IAV. Functional studies revealed that disruption of MALAT1 expression inhibited IAV replication, whereas overexpression of certain MALAT1 fragments enhanced the virus replication. Using ribosome profiling, mass spectrometry, and antibody validation, we identified a micropeptide (miPEP-52) encoded by an RNA fragment of MALAT1, which was endogenously expressed and upregulated by IAV infection. Moreover, we observed that miPEP-52 strongly enhanced the replication of IAV. Mutating the miPEP-52 start codon or deleting its coding sequence from the MALAT1 RNA fragment abolished these effects.