Lack of sleep incurs physiological costs that include increased inflammation and alterations in the hypothalamic-pituitary-adrenal (HPA) axis. Specifically, sleep restriction or deprivation leads to increased pro-inflammatory cytokine expression and elevated glucocorticoids in rodent models, but whether birds exact similar costs is unknown. In this study, we examined whether zebra finch (Taeniopygia guttata), an avian model species, exhibits physiological costs of sleep loss using a novel automated sleep fragmentation/deprivation method; a horizontal wire sweeps across a test cage to disrupt sleep every 120 s. We measured pro-inflammatory (IL-1β and IL-6) and anti-inflammatory (IL-10) cytokine gene expression in the periphery (fat, liver, spleen, and heart) and brain (hypothalamus, hippocampus, and apical hyperpallium) of captive finches after 12 h of exposure to a moving or stationary (control) bar during the night or the day. Plasma corticosterone, body mass, and behavioral profiles were also assessed. We predicted that birds undergoing sleep loss would exhibit elevated pro-inflammatory and reduced anti-inflammatory gene expression in brain and peripheral tissues compared with control birds. In addition, we predicted an increase in plasma corticosterone levels after sleep loss. As predicted, sleep loss increased pro-inflammatory gene expression, specifically in adipose tissue (IL-6), spleen (IL-1), and hippocampus (IL-6), but a decrease in anti-inflammatory expression (IL-10) was not detected. However, sleep loss elevated baseline concentrations of plasma corticosterone. Taken together, these results suggest that a diurnal, non-migratory songbird is sensitive to the costs of sleep loss.