Cancer genome profiling testing (multigene testing) methods have been clinically applied to detecting alterations of numerous cancer-associated genes, and these new methods are widely used in pediatric cancer. In pediatric cancer, these comprehensive methods play an important role not only in identifying a biomarker for therapeutic targets, but also in definitive diagnosis and prognosis prediction. The precision medicine approach is expected to contribute to minimizing complication without compromising relapse risk. It should also be noted that a certain fraction of children with cancer have pathogenic variants in cancer predisposition genes. Thus, genetic counseling and surveillance system should be established. To utilize complex results of genetic analysis, medical interpretation should be reviewed by an “expert panel”. Considering the uniqueness of pediatric cancer, an exceptional process of consultation is permitted. As a future perspective of pediatric cancer genomic medicine, expansion of drug availability, development of optimal multigene testing, and education are issues to be solved.