Spliceosome mutations are common in MDS and AML, yet the oncogenic changes due to these mutations have not been identified. A global analysis of exon usage in AML samples revealed distinct molecular subsets containing alternative spliced isoforms of inflammatory and immune genes. IRAK4 was the dominant alternatively spliced isoform in MDS/AML and is characterized by a longer isoform that retains exon 4, encoding a protein, IRAK4-Long (L) that assembles with the Myddosome, results in maximal activation of NF-κB, and is essential for leukemic cell function. Expression of IRAK4-L is mediated by mutant U2AF1 and is associated with oncogenic signaling in MDS/AML. Inhibition of IRAK4-L abrogates leukemic growth, particularly in AML cells with higher expression of the IRAK4-L isoform. Collectively, mutations in U2AF1 induce expression of therapeutically targetable “active” IRAK4 isoforms and provide a genetic link to activation of chronic innate immune signaling in MDS and AML.