Human endogenous retroviruses (HERVs), the remains of retroviruses infection in our ancestors’ germline cell over millions of years, take up about 8% of the human genome in total. HERV transcription has been detected in various cancers and diseases. However, the interaction between HERV expression and viral infection has not been fully elucidated. Here, we provided the first transcriptional profile of HERVs in dengue virus serotype 2 (DENV-2) infected A549 cells by using high-throughput RNA sequencing. The results showed that a number of HERVs and human genes were significantly differentially expressed in response to DENV-2 infection. Further bioinformatic analyses indicated a correlation between HERVs and human genes. In particular, the genes near the HERVs activated by dengue infection were dominantly enriched in the antiviral immune response. Taken together, our findings suggest that activated HERVs may be involved in the cellular immune response to viral infection by coexpressing with nearby host genes.