In this work, we performed a 3D‐QSAR study on a dataset of benzimidazole‐indazole‐derived molecules reported as FLT3 inhibitors for the treatment of acute myeloid leukemia (AML). This study led to the design of six new molecules with better FLT3 inhibitory activity than the reference inhibitor (gilteritinib) and the synthesized template molecule (M20). The designed molecules are screened for their drug‐like and ADMET proprieties. The obtained results enabled us to select three molecules as the best candidate FLT3 inhibitors. Molecular docking and MM‐GBSA calculations show that the three molecules are more localized and targeted in the FLT3 active site compared to gilteritinib and M20 molecules. Through molecular dynamics simulations, the insertion of the three designed molecules in the FLT3 active site leads to stable complexes during the simulation period. Finally, the three newly designed molecules represent an interesting proposal for the development of drugs against AML.