Studies suggest that musical training enhances spatial-temporal reasoning and leads to greater learning of mathematical concepts. The aim of this prospective study was to verify the efficacy of a Non-Instrumental Musical Training (NIMT) on the Numerical Cognition systems in children with low achievement in math. For this purpose, we examined, with a cluster analysis, whether children with low scores on Numerical Cognition would be grouped in the same cluster at pre and post-NIMT. Participants were primary school children divided into two groups according to their scores on an Arithmetic test. Results with a specialized battery of Numerical Cognition revealed improvements for Cluster 2 (children with low achievement in math) especially for number production capacity compared to normative data. Besides, the number of children with low scores in Numerical Cognition decreased at post-NIMT. These findings suggest that NIMT enhances Numerical Cognition and seems to be a useful tool for rehabilitation of children with low achievement in math.