Human immunodeficiency virus (HIV) affects millions of people across the globe. Despite the introduction of powerful anti-viral therapies, one factor confounding viral elimination is the ability of HIV to remain latent within the host genome. Here, we perform a network analysis of the viral reactivation process using human gene expression profiles and curated databases of both human-human and human-HIV protein interactions. Based on this analysis, we report the identification of active pathways in both the latent and early phases of reactivation. These active pathways suggest host functions that are altered and important for HIV pathogenesis.