This study aimed to: (i) analyze fat mass and physical fitness variations among age-groups and playing positions, and (ii) explore the relationship between fat mass and physical fitness in youth male soccer players. A total of 66 players from under-16, under-17, and under-19 were tested. Body mass, skinfolds, countermovement jump (CMJ), single-leg triple hop jump (SLTH), bilateral triple hop jump (BTH), and yo-yo intermittent recovery Level 2 (YYIR-2) were assessed. A two- and one-way ANOVA were conducted, and the effect size was measured. Interactions were found in skin folds and fat mass. The under-19 group was taller, heavier, with a greater BMI and muscle mass than the under-16 group. They also exceeded the under-16 and under-17 in SLTH, BTH, and YYIRT-2. The under-17 group jumped higher and longer than under-16 group. Goalkeepers were taller and heavier than the midfielders. Central defenders were taller and had more muscle mass than midfielders and were heavier than the midfielders and wingers. The wingers jumped higher than the midfielders and showed better YYIRT-2. BMI was small correlated with YYIRT-2 and moderately with CMJ. Fat mass had a moderate negative correlation with CMJ and YYIRT-2. Muscle mass largely correlated with CMJ, UTH, very large with BTH and moderate with YYIRT-2. Summarily, with increasing age, better performances and body compositions were registered. Muscle mass better influences performance than body fat. Body composition can distinguish players positions.