Risk assessments have identified prey limitation as one of the strongest risk factors for juvenile salmon migration survival under climate change. In British Columbia, Canada, juvenile Chinook salmon (Oncorhynchus tshawytscha) may experience prolonged periods of food deprivation during their marine entry and first marine winter. In this study we conducted a lab-based food deprivation and refeeding experiment to assess the physiological consequences of starvation and identify transcriptional responses to develop mRNA-based biomarkers for food limitation in the gill of juvenile Chinook salmon. Throughout the experiment, fish were held at both summer (16oC; marine entry) and winter (8oC; overwintering) temperatures and were sampled at least every 2 weeks collecting physiological data (condition factor, hepatosomatic index, morphometrics) as well as liver and gill tissue for RNA-sequencing. As expected, both food-deprivation treatments demonstrated significant differences from their fed counterparts with decreases in condition factor and hepatosomatic index with 14 to 28 days, respectively. The 16oC acclimation treatment was the first to reach a starvation endpoint (10% mortality) by 35 days, with the 8oC treatment persisting until 56 days (20% reduced condition factor). During refeeding, condition factor returned rapidly in both acclimation treatments, 9-12 days post feed introduction. Further, hepatosomatic index recovered within 3 days and increased up to 2.5-fold when compared to unfasted counterparts by days 12-21 of the refeeding process. Conserved transcriptional responses between 8oC and 16oC treatments will be discussed in the context ofpathways modified by starvation, and candidate biomarkers for nonlethal screening in wild juvenile Chinook salmon.