Motor, psycho-emotional, cognitive and social variables, plus other factors like gender, influence how schoolchildren perceive their motor competence level. By means of a hierarchical linear regression analysis, this longitudinal study aimed to determine the predictive value that coordination, anxiety, and self-esteem at the age of 9 years can have on the self-perceived motor competence variable at the age between 11 and 12 years. Data collection was performed with 224 pupils at a first time point with grade-4 Primary Education (PEd) pupils (mean age 9.11 ± 0.32 years) and a second time point with grade-6 PEd pupils (11.49 ± 0.50 years). The results evidenced that coordination, anxiety, and self-esteem at the age of 9 years predicted self-perceived motor competence at ages between 11 and 12 years. Gender differences were also observed in these results. For the female gender, age, coordination, and anxiety variables explained the variance for self-perceived motor competence. For the male gender, age, coordination, and self-esteem explained the variance for self-perception competence. This reveals the importance of more globally understanding self-perceived motor competence in PEd pupils considering the predictive role of psycho-emotional, motor, and socio-demographic variables based on gender.