Age-related human hematopoietic stem cell (HSC) exhaustion and myeloid-lineage skewing promote oncogenic transformation of hematopoietic progenitor cells into therapy-resistant leukemia stem cells (LSCs) in secondary acute myeloid leukemia (AML). While acquisition of clonal DNA mutations has been linked to increased rates of secondary AML for individuals older than 60 years, the contribution of RNA processing alterations to human hematopoietic stem and progenitor aging and LSC generation remains unclear. Comprehensive RNA sequencing and splice-isoform-specific PCR uncovered characteristic RNA splice isoform expression patterns that distinguished normal young and aged human stem and progenitor cells (HSPCs) from malignant myelodysplastic syndrome (MDS) and AML progenitors. In splicing reporter assays and pre-clinical patient-derived AML models, treatment with a pharmacologic splicing modulator, 17S-FD-895, reversed pro-survival splice isoform switching and significantly impaired LSC maintenance. Therapeutic splicing modulation, together with monitoring splice isoform biomarkers of healthy HSPC aging versus LSC generation, may be employed safely and effectively to prevent relapse, the leading cause of leukemia-related mortality. Display omitted •Splice isoform signatures distinguish normal and malignant progenitor cell aging•Pro-survival splice isoform switching is a feature of secondary AML LSC•Splice isoform biomarkers provide diagnostic and therapeutic targets for AML•Spliceosome modulators impair AML LSC maintenance in humanized pre-clinical models Crews et al. show that unique splice isoform signatures distinguish normal human HSC and progenitor cell aging from AML and MDS progenitors. Widespread deregulation of splicing factor gene expression typified AML progenitors and sensitized them to small-molecule splicing-targeted agents, supporting the utility of spliceosome modulation in leukemia stem cell eradication and anti-aging strategies.