The island fox (Urocyon littoralis) is native to 6 of the 8 Channel Islands of California, USA. The species experienced a population decline in the 1990s but recovered after predatory golden eagles (Aquila chrysaetos) were relocated and feral pigs (Sus scrofa), a main food source for the eagles, were removed. As part of an ongoing conservation program, the National Park Service conducts yearly health surveys on foxes residing on Santa Rosa and San Miguel islands. In this study, we document non‐invasive measures of stress and nutritional status from fecal samples collected during surveys from 2009 to 2015. We collected samples defecated in traps overnight or during handling and measured concentrations of glucocorticoid (GC) and triiodothyronine (T3) metabolites using validated assays. We used generalized linear mixed models to assess the relationships between hormones, season, island, age class, sex, body condition, reproductive status, and ectoparasite presence. Overall, males had marginally lower fecal T3 concentrations than females. Concentrations of both hormones positively correlated with body condition. Fecal GC production varied seasonally; concentrations were highest from December to February and declined through the summer and fall. During summer, younger females and those with signs of recent reproduction had higher fecal GC concentrations than older females or those without evidence of reproduction. Fecal T3 concentrations did not vary in relation to season, age, or reproductive status, but on San Miguel Island were positively correlated with ectoparasite presence. There were no other significant differences between islands. Our results provide hormone data for island foxes and demonstrate that production varies in relation to seasonal and biological factors. These reference data will serve as a comparison for future health surveys and allow managers to identify factors associated with increased stress or reduced nutritional state. © 2019 The Wildlife Society.