During outmigration, juvenile Chinook salmon leave the cooler upper stretches of their natal rivers and make the journey to the ocean, often experiencing increased water temperatures as they travel downstream. Dams, a common feature of many California Rivers, can further alter the natural temperature regime experienced by salmon. Thermally stressed juvenile Chinook exhibit behavioral and physiological changes, which may affect their survival during outmigration. To investigate the effect of short periods of thermal stress at a transcriptional level, we performed RNAseq on juvenile Chinook gill tissue following acute thermal stress. Central Valley fall-run Chinook were collected from the Merced River hatchery as eggs and raised at optimal temperature conditions in the laboratory for approximately five months. In this experiment, individuals from eleven parental crosses raised at 12 degrees Celsius were evenly divided and exposed to either 12, 15, 18, 21, or 25 degree Celsius water for three hours, followed by a one hour recovery period at the acclimation temperature and then tissue collection. Three replicates were performed at each temperature. Pooled RNA extracted from gill tissue was used to create sequencing libraries using the Illumina TruSeq RNA kit and sequenced on the Illumina HiSeq2000. The observed patterns of differential gene and inferred cellular changes that occur during short thermal stresses are discussed. In the future, expression profiles at the different temperatures may be used to help identify thermal stress in the field.