Sea Turtles lay eggs at relatively deep depths on beaches. Although nest emergence is known to be costly for hatchlings, little is known about the positive aspects of emergence. In this study, we investigated the effects of emergence on hatchling phenotypes of Loggerhead Sea Turtles (Caretta caretta) in the North Pacific population. We placed the Loggerhead eggs in an incubator (incubator group) and relocated some eggs to a sand tank after the pip was confirmed (emergence group). Immediately after emergence was confirmed in the emergence group, we compared the morphology, terrestrial locomotor performance, and swimming performance of the two groups at the same time. Results showed that hatchlings in the emergence group were smaller than those in the incubator group. Notably, most members of the emergence group were able to completely traverse a 3-m course within 3 min, whereas no members of the incubator group could traverse the course. The emergence group had greater swimming performance than the incubator group. Taken together, these results suggest that emergence may have a positive effect on locomotor performance. Sea turtle nests are occasionally relocated for conservation purposes, and our results suggest that such egg management practices can alter hatchling phenotypes.