This study investigated whether enhanced rhythm training improves literacy development and working memory performance in pupils in the first and second year of school. According to recent literature, we hypothesized that rhythm-focused training could be effective for children with reading difficulties. Pupils aged 6 to 8 years participated in the study, implemented as part of regular school music lessons. Children were divided into an experimental group that received enhanced rhythm training and a control group that received an equivalent amount of music instruction but without enhanced rhythm training. The intervention was delivered once a week for three months (13 lessons in total). The test battery included pre- and post-measures (0 and 3 months, respectively) with literacy and working memory assessment, and follow-ups (8 and 20 months) with literacy assessment. There was no statistically significant difference between the groups in literacy skills after training. However, there was a moderate improvement in working memory performance for the experimental, but not the comparison group. In a post hoc analysis, we found an effect in a subgroup of lower starting-level readers, as the increase in literacy development of these students was statistically significant in the experimental, but not in the comparison group.