Sedentary screen media usage is currently the most popular leisure time sedentary behaviour among adolescents and is associated with multiple adverse health consequences. A growing body of evidence has suggested that screen media usage could also influence academic performance, showing inconclusive results. Therefore, the aim of the present study was to analyse the association between sedentary screen media usage and academic performance in physically active adolescents. A total of 264 adolescents from the DADOS (Deporte, ADOlescencia y Salud) study were included in the analyses. Sedentary screen media usage was self-reported by adolescents (i.e., time spent in video games, internet, mobile phone and television). Academic performance was assessed through the Science Research Associates Test of Educational Abilities for assessing cognitive abilities (i.e., verbal, numeric, reasoning and global), and through the final school grades (i.e., math, language and grade point average). Our results show that sedentary internet use time was inversely associated with school grades, reasoning ability and overall cognitive ability, and mobile phone use time was negatively related to grade point average. These findings suggest that programs aimed to promote the responsible use of new technologies among youth may result beneficial for academic performance.