The field of eusocial insect innate immune response to viral pathogens has remained largely understudied despite its implications in biological control and conservation. Such is the case with the pathogenesis of the pest species the red imported fire ant Solenopsis invicta (Hymenoptera: Formicidae). Imported fire ants are major insect pests, and the red imported fire ant pathogens Solenopsis invicta viruses are promising biological control candidates. To expand upon the thin knowledge base on eusocial insect immune response to viral pathogens and to develop a more complete picture for fire ant biological control via viral natural enemies, we compared the transcriptome of infected and uninfected colonies. We infected laboratory S. invicta colonies with Solenopsis invicta virus-3, sequenced the transcriptome of both infected and uninfected colonies, and report differential expression in innate immune response pathways. Differences are discussed in relation to innate immune pathways of S. invicta in response to viral pathogens and their potential application for biological control.