Asymmetric cell division results in two distinctly fated daughter cells. A molecular hallmark of asymmetric division is the unequal partitioning of cell fate determinants. We have previously established that growth factor signaling promotes protein depalmitoylation to foster polarized protein localization, which in turns drives migration and metastasis. Here, we report protein palmitoylation as a key mechanism for the asymmetric partitioning of the cell fate determinants Numb and β-catenin through the activity of the depalmitoylating enzyme APT1. Using point mutations, we show specific palmitoylated residues on Numb are required for asymmetric localization. By live-cell imaging, we show that reciprocal interactions between APT1 and the Rho-family GTPase CDC42 promote the asymmetric localization of Numb and β-catenin to the plasma membrane. This in turn restricts Notch- and Wnt-responsive transcriptional activity to one daughter cell. Moreover, we show altering APT1 expression changes the transcriptional signatures of MDA-MB-231 triple receptor–negative breast cancer cells similarly to changes in Notch and β-catenin–mediated Wnt signaling. We also show that loss of APT1 depletes a specific subpopulation of tumorigenic cells in colony formation assays. Together, our findings demonstrate that APT1-mediated depalmitoylation is a major mechanism of asymmetric cell division maintaining Notch and Wnt-associated protein dynamics, gene expression, and cellular functions.