Long non-coding RNAs (lncRNAs) are critical regulators of various biological processes, yet their roles in chicken host-virus interactions remain largely unknown. This study investigated the impact of influenza A virus (IAV) H9N2 infection on the expression of two lncRNAs, Lnc9101 and Lnc8475, and the regulatory roles of these lncRNAs in the innate immune response. The results demonstrated that the expression of both lncRNAs were significantly upregulated in H9N2-infected chickens and could be induced by viral genomic RNA, poly (I:C) or LPS. Disruption of Lnc9101 expression in DF-1 cells enhanced the IAV replication, while its overexpression suppressed it. Conversely, Lnc8475 had the opposite effect on the IAV replication compared with Lnc9101. Silencing Lnc8475 expression in DF-1 cells attenuated IAV replication, while its overexpression promoted viral replication. Furthermore, we found that both lncRNAs regulated the expression of type I and type III interferons (IFNs), thereby affecting multiple interferon-stimulating genes (ISGs) expression and STAT1 activation upon IAV infection. Moreover, Lnc9101 knockdown impaired the expression of TLR7 and MDA5 and reduced IRF7 phosphorylation, whereas Lnc8475 knockdown promoted the expression of TLR3 and TLR7. In summary, Lnc9101 inhibits IAV replication by positively regulating the innate immune response, whereas Lnc8475 promotes IAV replication by suppressing it. These findings suggest that LncRNA9101 and Lnc8475 play important roles in pattern recognition receptors (PRRs)-dependent innate immune signaling and antiviral responses, advancing a better understanding of lncRNA functioning in chickens.