Emerging evidence has revealed that long noncoding RNAs (lncRNAs) are involved in hepatitis B virus (HBV) replication. However, the roles of most lncRNAs in HBV replication remain unclear. In the present study, we determined that HNF4A-AS1 was downregulated by HBV during infection. Interestingly, HNF4A-AS1 inhibited HBV transcription and replication in human hepatoma cells. Mechanistically, HNF4A-AS1 inhibited HBV replication by promoting TLE4 expression at the transcriptional level. The TLE4 WD-repeat domain is required for TLE4-mediated anti-HBV activity. Collectively, our findings have uncovered a negative feedback mechanism underlying HBV replication and HNF4A-AS1 expression and identify HNF4A-AS1 as a novel host restriction factor in HBV replication, providing a potential therapeutic target for HBV treatment.