The neurogenomic mechanisms modulating cooperation are largely unknown, and previous work has been largely constrained to considering few genes in limited neurological space. Here we leverage transcriptomic and behavioral data on birds that perform cooperative courtship displays to better understand the mechanisms underlying cooperative behaviors. Males of the neotropical wire-tailed manakin (Pipra filicauda) form cooperative display coalitions, and their cooperative behaviors are modulated by testosterone in a status-specific manner: Testosterone promotes cooperation in non-territorial birds, but suppresses it in territory holders. To understand the neurogenomic basis of individual and status-specific regulation of cooperative display behavior, we profiled gene expression in 10 brain nuclei and two key endocrine tissues known to regulate social behavior. We associated gene expression with each bird's detailed behavioral and endocrine profile derived from years of repeated measures taken from free-living birds in the Ecuadorian Amazon. We found distinct landscapes of constitutive gene expression were associated with social status, testosterone phenotype, and cooperation, reflecting the modular organization and engagement of neuroendocrine tissues. Sex-steroid and neuropeptide signaling appear important in mediating status-specific relationships between testosterone and cooperation, and suggests shared regulatory mechanisms with male aggressive and sexual behaviors. We also find that systemic gene expression across the brain that could form the basis of social status-specific neuro-physical phenotypes, which are potentially mediated by testosterone and growth hormone. Overall, our findings provide new, systems-level insights into the mechanisms of cooperative behavior, and suggest differences in neurogenomic state form the basis for individual differences in behavioral phenotypes.