Variation in early life history traits often leads to differentially expressed morphological and behavioral phenotypes. We investigated whether variation in egg size and emergence timing influence subsequent morphology associated with migration timing in juvenile spring Chinook Salmon, Oncorhynchus tshawytscha. Based on evidence for a positive relationship between growth rate and migration timing, we predicted that fish from small eggs and fish that emerged earlier would have similar morphology to fall migrants, while fish from large eggs and individuals that emerged later would be more similar to older spring yearling migrants. We sorted eyed embryos within females into two size categories: small and large. We collected early and late‐emerging juveniles from each egg size category. We used landmark‐based geometric morphometrics and found that egg size appears to drive morphological differences. Egg size shows evidence for an absolute rather than relative effect on body morphology. Fish from small eggs were morphologically more similar to fall migrants, while fish from large eggs were morphologically more similar to older spring yearling migrants. Previous research has shown that the body morphology of fish that prefer the surface or bottom location in a tank soon after emergence also correlates with the morphological variations between wild fall and spring migrants, respectively. We found that late‐emerging fish spent more time near the surface. Our study shows that subtle differences in early life history characteristics may correlate with a diversity of future phenotypes.