Fever during influenza A virus (IAV) infection is triggered by the innate immune response. Various factors contribute to this response, including IAV mini viral RNAs (mvRNA), which trigger RIG-I signaling when their replication and transcription are dysregulated by template loops (t-loop). While fever is a symptom of the infection, it also alters the environment in which virus replicates. This changing environment may impact the viral infection cycle and in turn disease outcome. Here we show that IAV infection at temperatures that simulate fever leads to increased mvRNA synthesis and antiviral signaling. Mathematical modeling and experimental analyses reveal that differential IAV nucleoprotein and RNA polymerase production underlies the increased mvRNA level. Moreover, at the higher infection temperature mvRNAs with dysregulating t-loops contribute most to the innate immune activation. We propose that fever-enhanced mvRNA production is a self-amplifying feedback loop that may affect infection outcome.