Interference competition over food and territory can shape population structure and habitat use within and between species. The introduction of invasive species often leads to novel competitive interactions over shared resources and invaders can eventually exclude the native species from preferred habitats. Invasive brook trout (Salvelinus fontinalis) introduced to northern Europe have excluded native brown trout (Salmo trutta) from numerous headwater streams. The fact that invasive brook trout can displace the more aggressive brown trout is puzzling. However, the earlier spawning and hatching of brook trout, compared to brown trout, may lead to unequal competition due to size advantage and prior resident status of brook trout at the fry stage. In this study, we examine the effect of competition between brown trout and brook trout using the natural size distribution of the two species. In two consecutive experiments, we first measured space use and feeding of a fry (age 0+) in the presence of a juvenile (age 1+). In experiment 2, we assessed territorial interactions between the species at the fry stage (age 0+) and if smaller brown trout could compensate the disadvantage by manipulating residence duration. Fry of brook trout feed sooner and spend more time close to the larger individual than brown trout fry. We also found that brook trout fry won most territorial contests against brown trout, and that increased residence duration led to longer and more aggressive interactions. The results suggest that smaller brown trout are displaced to suboptimal habitats in the presence of a larger brook trout. Therefore, the later emergence from gravel beds resulting in the naturally occurring size disadvantage of brown trout at the fry stage may lead to unequal territorial interactions that could explain why brown trout are displaced from preferred habitats in sympatry with brook trout.