The use of magnetoencephalography (MEG) to understand alterations in brain development in children has increased rapidly over the past two decades. Investigators have argued that MEG is an ideal neuroimaging tool for children because the technology is quiet and it provides high-density sensor systems. This participant-friendly technology has led to exploration of the use of MEG to identify biomarkers for atypical brain development to facilitate early diagnosis and intervention. Prior studies provide evidence that MEG is sensitive to a number of pediatric clinical disorders demonstrated through significant differences (e.g., latency, amplitude, spectral power) in children with autism spectrum disorder, children born prematurely, and children with fetal alcohol spectrum disorder, to name a few. At the same time, differences in age range, stimulus parameters, and study population characteristics contribute to variability in results across independent laboratories. While the current studies provide strong evidence for the sensitivity of MEG to identify brain abnormalities in children, replication studies are needed to validate biomarkers of atypical brain development to identify children at risk for atypical brain development. Additional studies are also needed to understand the dynamic changes in these brain markers across the age spectrum. Finally, future directions include gaining a broader understanding of typical and atypical brain development to identify neural targets for intervention.