Playing a musical instrument engages various sensorimotor processes and draws on cognitive capacities collectively termed executive functions. However, while music training is believed to associated with enhancements in certain cognitive and language abilities, studies that have explored the specific relationship between music and executive function have yielded conflicting results. As part of an ongoing longitudinal study, we investigated the effects of music training on executive function using fMRI and several behavioral tasks, including the Color-Word Stroop task. Children involved in ongoing music training (N = 14, mean age = 8.67) were compared with two groups of comparable general cognitive abilities and socioeconomic status, one involved in sports ("sports" group, N = 13, mean age = 8.85) and another not involved in music or sports ("control" group, N = 17, mean age = 9.05). During the Color-Word Stroop task, children with music training showed significantly greater bilateral activation in the pre-SMA/SMA, ACC, IFG, and insula in trials that required cognitive control compared to the control group, despite no differences in performance on behavioral measures of executive function. No significant differences in brain activation or in task performance were found between the music and sports groups. The results suggest that systematic extracurricular training, particularly music-based training, is associated with changes in the cognitive control network in the brain even in the absence of changes in behavioral performance.