Background and objective: Chemotherapy plays an important role in the treatment of leukemia. Multidrug resistance (MDR) induced by chemotherapy always leads to treatment failure and disease recurrence. MicroRNAs (miRNAs) have been verified as crucial components in carcinogenesis, including chemo-resistance of tumor cells, which has not been fully understood. In this study, we aimed to identify the potential candidate miRNA, miR-1246, and reveal its regulatory role in chemo-resistance of leukemia cells. Methods: Candidate miRNAs were selected by microarray analysis, screened by bioinformatics tools and verified by reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Chemo-resistant phenotypes, including cell viability, apoptosis, adriamycin (ADM) efflux and in vivo oncogenicity of leukemia cells following transfected with miR-1246 mimics or inhibitor were checked with or without ADM treatment to make clear the relationship between miR-1246 and chemo-resistance. RT-qPCR, western blot and dual luciferase reporter assay were performed to measure the expression of related genes and address the potential regulatory mechanism of miR-1246 in chemo-resistance. Results: The expression of miR-1246 was significantly higher in chemo-resistant leukemia K562/ADM cells, HL-60/RS cells and recurrent primary leukemia cells. Loss of miR-1246 inhibited proliferation, induced apoptosis, altered cell cycle distribution, inhibited ADM efflux in chemo-resistant leukemia cells, while overexpression of miR-1246 showed the opposite role in chemo-sensitive leukemia cells. Both bioinformatics prediction and luciferase assay indicated that AXIN2 and glycogen synthase kinase 3 beta (GSK-3β) were the direct targets of miR-1246 in leukemia cells. Inhibition of miR-1246 could up-regulate AXIN2 and GSK-3β and inactivate Wnt/β-catenin pathway, accompanied with inhibiting the expression of β-catenin and further influencing the expression of P-glycoprotein (P-gp) in the chemo-resistant leukemia cells. Conclusions: Chemo-resistant ability of MDR leukemia cells is attenuated by loss of miR-1246 via negatively regulating AXIN2 and GSK-3β to inactivate Wnt/β-catenin pathway and suppress P-gp expression, these mean that targeting miR-1246-AXIN2/GSK-3β-Wnt/β-catenin axis may be beneficial to overcome the chemo-resistance in relapse and refractory leukemia patients.