An extensive literature has investigated the impact of musical training on cognition and academic achievement in children and adolescents. However, most of the studies have relied on cross-sectional designs, which makes it impossible to elucidate whether the observed differences are a consequence of the engagement in musical activities. Previous meta-analyses with longitudinal studies have also found inconsistent results, possibly due to their reliance on vague definitions of musical training. In addition, more evidence has appeared in recent years. The current meta-analysis investigates the impact of early programs that involve learning to play musical instruments on cognitive and academic skills, as previous meta-analyses have not focused on this form of musical training. Following a systematic search, 34 independent samples of children and adolescents were included. All the studies had pre-post designs and, at least, one control group. Overall, we found a small but significant benefit (g = 0.24) with short-term programs, regardless of whether they were randomized or not. In addition, a small advantage at baseline was observed in studies with self-selection (g = 0.28), indicating that participants who had the opportunity to select the activity consistently showed a slightly superior performance prior to the beginning of the intervention. Our findings support a nature and nurture approach to the relationship between instrumental training and cognitive performance. Nevertheless, evidence from well-conducted studies is still scarce and more studies are necessary to reach firmer conclusions.