Recently, treatment with BET (bromodomain and extraterminal) protein antagonist (BA) such as JQ1 has been shown to inhibit growth and induce apoptosis of human AML cells, including those expressing FLT3-ITD. Here, we demonstrate that co-treatment with JQ1 and the FLT3 tyrosine kinase inhibitor (TKI) ponatinib or AC220 synergistically induce apoptosis of cultured and primary CD34+ human AML blast progenitor cells (BPCs) expressing FLT3-ITD. Concomitantly, as compared to each agent alone, co-treatment with JQ1 and the FLT3-TKI caused greater attenuation of c-MYC, BCL2 and CDK4/6. Simultaneously, co-treatment with JQ1 and the FLT3-TKI increased the levels of p21, BIM and cleaved PARP, as well as mediated marked attenuation of p-STAT5, p-AKT and p-ERK1/2 levels in AML BPCs. Conversely, co-treatment with JQ1 and FLT3-TKI was significantly less active against CD34+ normal bone marrow progenitor cells. Knockdown of BRD4 by shRNA also sensitized AML cells to FLT3-TKI. JQ1 treatment induced apoptosis of mouse Ba/F3 cells ectopically expressing FLT3-ITD with or without FLT3-TKI resistant mutations F691L and D835V. Compared to the parental human AML FLT3-ITD-expressing MOLM13, MOLM13-TKIR cells resistant to AC220 were markedly more sensitive to JQ1-induced apoptosis. Further, co-treatment with JQ1 and the pan-histone deacetylase inhibitor (HDI) panobinostat synergistically induced apoptosis of FLT3-TKI resistant MOLM13-TKIR and MV4-11-TKIR cells. Collectively, these findings support the rationale for determining the in vivo activity of combined therapy with BA and FLT3-TKI against human AML cells expressing FLT3-ITD or with BA and HDI against AML cells resistant to FLT3-TKI.