Background: Pediatric non-Down Syndrome Acute Megakaryoblastic Leukemia (non-DS-AMKL) is a rare subtype of Acute Myeloid Leukemia (AML) arising from primitive megakaryocytes and is associated with poor outcomes. Given its high incidence of relapse, this subpopulation of children is frequently referred for allogeneic hematopoietic stem cell transplant (allo-HSCT) in first complete remission (CR1). Objectives: The objective of this study was to describe the clinical outcomes of non-DS-AMKL pediatric patients in a large, single-institution cohort. Methods: A retrospective review of the medical records of thirty-six patients diagnosed with non-DS-AMKL treated at Texas Children’s Hospital from 2000 to 2022 was conducted. Results: Twenty-nine patients were included in the analysis, with cohorts defined by intention to treat. Twelve patients received chemotherapy only during upfront therapy, and seventeen received upfront HSCT. The 5-year overall survival (OS) and disease-free survival (DFS) for the entire cohort were 19.1% and 24.1%, respectively, with a median survival of 17.4 months. A higher percentage of patients in the chemotherapy-only group had relapsed/refractory disease at death (chemotherapy only, n = 9; HSCT, n = 8). However, 5-year OS and DFS were similar for both groups (OS = 18.8% vs. 31.3%, p = 0.58; DFS = 37.6% vs. 22.2%, p = 0.51). Relapse was the leading cause of death (5-year cumulative incidence of relapse (CIR) 0.78). Treatment with allo-HSCT did not improve outcomes due to the high CIR, even after HSCT in CR1. Conclusions: These dismal outcomes highlight the need for development and incorporation of novel targeted agents into upfront therapy or in the post-HSCT setting for patients with this challenging disease.