B-cell acute lymphoblastic leukemia (B-ALL) is a heterogeneous disease wherein cytogenetics comprises an independent prognostic factor. Cytogenetic subgroups like B-ALL with t(9;22), MLL rearrangement, hypodiploidy, and Ph-like ALL are stratified as high-risk and are treated on the high-risk regimen. However, a subset that does not fall into a specific cytogenetic risk groups, is classified as cytogenetics NOS (Not Otherwise Specified) and might receive suboptimal chemotherapy. Identifying genetic abnormalities that are susceptible to targeted therapy can help improve outcomes. Therefore, with the intent to report cytogenetic data potentially useful for targeted therapy, we report a novel JAK2 amplification in a cytogenetically complex pediatric B-ALL case with early relapse.