The main purpose of this study was to analyze the internal structure and measurement invariance across gender and age of the Strengths and Difficulties Questionnaire (SDQ), self-reported version, in Spanish adolescents. The sample consisted of 1,547 participants, 606 were male (39.1%), with a mean age of 15.15 years (SD = 1.99). Results from the confirmatory factor analysis showed a five-factor model and a bifactor model with correlated errors added as the most appropriate. Nevertheless, the bifactor model displayed lower and non-significant factor loadings. The hypothesis of measurement invariance of the SDQ scores across gender and age was supported. The level of internal consistency of the Total difficulties score was .84, ranging between .71 and .75 for the SDQ subscales. The study of the psychometric properties showed that the Spanish version of the SDQ, self-reported form, seems to be an adequate tool for the screening of emotional and behavioural problems during adolescence. Future research should analyze the internal structure of the SDQ in other regions and testing the measurement invariance across cultures.