Malignant ectomesenchymoma (MEM) is an exceedingly rare pediatric sarcoma, with predilection for infants and young children, composed of dual malignant mesenchymal and neuroectodermal components. Microscopically, MEM displays areas of rhabdomyosarcoma (RMS) with intermixed neuronal/neuroblastic foci. The molecular alterations MEM and its relationship with embryonal RMS (ERMS) and malignant peripheral nerve sheath tumor (MPNST) have not yet been elucidated. In this study we use whole transcriptome sequencing in 2 MEM index cases with available frozen tissue, followed by screening the identified genetic abnormalities in 5 additional cases. No candidate fusion genes were detected by FusionSeq analysis, however, the mutation detection algorithms revealed HRAS and PTPRD hot-spot mutations in both index cases, with one case harbouring an additional FBXW7 mutation. As these mutation profiles have been previously described in ERMS we have tested their incidence in a control group of 7 age-matched ERMS. Additionally, the gene signature of MEM was compared to that of RMS, MPNST and neuronal lineage. All 7 MEM patients were male, with a mean age of 7.5 months (range 0.6–17 mo). All except one occurred in the pelvis/urogenital region. Most cases showed ERMS elements, with occasional spindle or undifferentiated/round cell areas. The intermixed neuroectodermal components were mostly scattered ganglion cells, ganglioneuroma, or ganglioneuroblastoma. By Sanger sequencing, 6 of 7 (86%) MEMs had HRAS mutations, with no additional case harboring PTPRD or FBXW7 mutations. The only case lacking HRAS mutation showed neuroblastic micronodules without ganglion cells. The trimethylation at lysine 27 of histone H3 (H3K27me3) expression, typically lost in MPNST, was retained in all cases. In the control ERMS group, 5 of 7 (71%) showed RAS mutations, equally distributed among NRAS, KRAS, and HRAS genes. The expression profiling of MEM showed upregulation of skeletal muscle and neuronal genes, with no significant overlap with MPNST. Our results of common HRAS mutations and composite gene signature with RMS and neuronal/ neuroblastic elements, suggest a closer genetic link of MEM to RMS rather than MPNST.