Recent research links disparities in children’s language-related brain function to poverty and its correlates. Such disparities are hypothesized to underlie achievement gaps between students from low-income families and more advantaged peers. Interventions that improve language-related brain function in low-income students exist, but evaluations of their implementation within high-poverty elementary schools do not. This comparison-group study evaluates whether implementation within high-poverty elementary schools of Harmony Project music-based mentoring, previously shown in randomized controlled research to improve language-related brain function and literacy in low-income students, might be associated with academic improvement for participants compared with non-participating peers. Standardized academic achievement scores were evaluated retrospectively for 2nd graders who opted into or out of Harmony Project (HP) at baseline (nHP = 218; nnon-HP = 862) for weekly music-based mentoring over 2 years. Adjusting for baseline scores, HP participation was associated with higher standardized scores for math (+17 points; ß = .06, p = .02) and English language arts (+26 points; ß = .08, p = .002). Importantly, students with the lowest prior achievement scores showed the greatest gains for both math (+33 points; ß =.13, p =.02) and English language arts (+39 points; ß =.14, p =.02). Implementation within high-poverty elementary schools of a program previously found to improve language-related brain function in low-income students was associated with significant academic improvement for participants, particularly those with the lowest prior levels of achievement. Findings support the hypothesis that disparities in children’s language-related brain function linked to poverty and its correlates may underlie achievement gaps.