Background: Numerous definitions of neighborhood exist, yet few studies have considered youth’s perceptions of neighborhood boundaries. This study compared youth-identified neighborhood (YIN) boundaries to census-defined neighborhood (CDN) boundaries, and determined how the amount of time spent and moderate-to-vigorous physical activity (MVPA) levels compared within both boundary types. Methods: Adolescents aged 11–14 years were asked to identify their neighborhood boundaries using a map. Objective location and physical activity data collected using Global Positioning System (GPS) devices and accelerometers were used to calculate the amount of time spent and MVPA within youth-identified and census-defined neighborhood boundaries. Paired bivariate analyses compared mean area (meters squared), percent of total time, daily MVPA (minutes), time density (minutes/m2) and MVPA density (minutes/m2) for both boundary types. Results: Youth-identified neighborhoods (1,821,705 m2) and census-defined neighborhoods (1,277,181 m2) were not significantly different in area, p = 0.30. However, subjects spent more time in youth-identified neighborhoods (80.3%) than census-defined neighborhoods (58.4%), p < 0.0001, and engaged in more daily MVPA within youth-identified neighborhoods (14.7 minutes) than census-defined neighborhoods (9.5 minutes), p < 0.0001. After adjusting for boundary area, MVPA density (minutes of MVPA per squared meter of area) remained significantly greater for youth-identified neighborhoods (2.4 × 10-4 minutes/m2) than census-defined neighborhoods (1.4 × 10-4 minutes/m2), p = 0.02. Conclusions: Adolescents perceive their neighborhoods to be similar in size to census-defined neighborhoods. However, youth-identified neighborhoods better capture the locations in which adolescents spend time and engage in physical activity. Asking adolescents to identify their neighborhood boundaries is a feasible and valuable method for identifying the spaces that adolescents are exposed to and use to be physically active