Background/Objectives: Children and adolescents spend a substantial amount of time being sedentary. The impact of prolonged sedentary patterns on fat distribution has not been elucidated especially in the context of physical activity level. Our objective is to examine the independent and joint associations of prolonged sedentary patterns and physical activity level with fat distribution among children and adolescents. Subjects/Methods: This included US children (8–11 years) and adolescents (12–19 years) from the National Health and Nutrition Examination Survey 2003–2006. Sedentary patterns comprise accelerometer-measured average sedentary bout duration and self-reported time of sitting watching TV/videos. Fat distribution (trunk and total fat percentage) was determined via dual X-ray absorptiometry. Results: Among 810 children and 2062 adolescents, average sedentary bout duration was associated with greater total and trunk fat percentages only among male children, after adjusting for moderate-to-vigorous physical activity (MVPA) level by accelerometer. Prolonged sitting watching TV/videos was associated with higher total and trunk fat percentages in male children and all adolescents, independent of levels of MVPA (all P for trend <0.05). Compared with ≤1 h/day, male children who spent ≥4 h/day sitting watching TV/videos had 4.43% higher trunk fat (95% CI, 1.69–7.17%), with similar associations for female (3.53%; 95% CI, 1.03–6.03%) and male adolescents (4.78%; 95% CI, 2.97–6.60%). About 13–17% children and adolescents spent <1 h on MVPA and ≥4 h sitting watching TV/videos per day. Compared with the most active group (MVPA ≥ 1 h/day and sitting watching TV/videos ≤1 h/day), trunk fat in this least active group was 6.21% higher in female children, 9.90% higher in male children, 6.84% higher in female adolescents, and 5.36% higher in male adolescents. Conclusions: Prolonged time spent on sitting watching TV/videos was associated with fat accumulation among children and adolescents, independent of physical activity level.