This study aimed to analyze the association between specific dimension (i.e., fitness, appearance, physical competence, physical strength, and self-esteem) of students’ physical self-concept (PSC) and their physical activity (PA) levels (i.e., intentions to be physically active and out-of-school PA levels perceived by students) and sedentary behavior (SB) (i.e., total sitting and screen time perceived by students). We also tested the role of students’ motivation (i.e., intrinsic motivation and amotivation) towards PA in these relationships. A total of 1998 Spanish male (n = 1003) and female (n = 995) secondary students, aged between 13 and 17 years (M = 14.92, SD = 0.87) from 22 schools, enrolled in third grade (n = 1081) and fourth grade (n = 917), completed the self-reported questionnaires. Five independent structural equation modeling (SEM) adjusted by students’ sex was used to examine the association between specific dimension of students’ PSC (i.e., fitness, appearance, physical competence, physical strength, and self-esteem) and self-reported PA and SB variables, and to test the role of students’ motivation in these relationships. Overall, most of students’ PSC dimension positively predicted students’ PA outcomes, and were negatively associated with SB. In addition, most of students’ PSC dimension were positively associated with intrinsic motivation, and negatively predicted amotivation. In turn, intrinsic motivation was a positive predictor of PA outcomes, and a negative predictor of SB, whereas amotivation was a negative predictor of PA outcomes and sitting time, and a positive predictor of screen time. Finally, from PSC dimensions, sex as a covariate was a positive predictor of intrinsic motivation and PA outcomes, and was a negative predictor of amotivation and sitting time. These findings suggest the importance of the specific dimensions of PSC perceived by adolescents on their motivational processes, and in turn, on their PA and SB outcomes.