Deregulation of the phosphatidylinositol-3-kinase (PI3K)/Akt signalling pathway is common in breast cancer and is frequently associated with resistance to both traditional chemotherapy and targeted drugs. There is a growing body of evidence indicating that a small subpopulation of self-renewing cells, the so called cancer stem cells (CSC), are responsible for the growth of drug resistant secondary tumors. As many CSCs have upregulated the PI3K/Akt signalling pathway, preclinical and clinical studies are addressing the inhibition of this axis to target drug resistance. We evaluated the susceptibility of breast CSCs to NVP-BKM120 (BKM120), a new generation of PI3K-specific inhibitor, when used individually or in combination with trastuzumab or RAD001 both in vitro and in vivo. For this, a stem-like cell population (SC) was enriched from breast cancer cell lines after mammosphere cultures. We demonstrated that BKM120 inhibits growth, generation of drug-resistant derivatives and SC formation in a panel of four breast cancer cell lines: MCF-7, MDA-MB-231, SK-BR-3 and CAL51. Importantly, BKM120 inhibits the PI3K/Akt signalling pathway in SCs from these cell lines. When BKM120 was used in combination with trastuzumab, a targeted therapy to treat HER2-positive breast cancer, we found synergistic cell growth inhibition, generation of drug resistant cells as well as SC formation from SK-BR-3 cells. Importantly, SK-BR-3 xenograft-derived tumors showed marginal growth when the drug combination was used. We also found a similar synergistic anticancer effect of BKM120 in combination with RAD001, an mTOR inhibitor, when treating triple-negative breast cancer cells in vitro and in both MDA-MB-231 and CAL51- mouse xenografts. Moreover, mouse data indicate that these drug combinations are well tolerated and provide the proof-of-concept and rationale to initiate clinical trials in both HER2-positive and triple-negative breast cancer.