Noonan syndrome (NS) is a multiple malformation syndrome where confirmation of diagnosis is difficult in the newborn. We report a case of a dysmorphic neonate who presented with bilateral chylous effusions and juvenile myelomonocytic leukemia where NS was confirmed by the presence of PTPN11 mutation. Juvenile myelomonocytic leukemia in NS is uncommon. The leukemia is usually self-limiting but lethal cases have been reported. Decisions regarding need for the treatment are unclear and further understanding of the genotype-phenotype relationships in PTPN11 mutations may help direct this.