The creation of a microvilli-rich apical luminal domain is essential for epithelial tissue morphogenesis and is closely coordinated with the formation of the apical junctional complex (AJC). De novo lumenogenesis, in which epithelial cells establish apical identity by directing apical cargo to an apical membrane initiation site (AMIS), has been studied extensively. However, the mechanisms behind AMIS formation and its progression into a luminal precursor remain poorly understood. In this study, we employed super-resolution imaging, correlative light and electron microscopy, and time-resolved proximity proteomics to explore the spatial, temporal, and molecular processes involved in apical lumen initiation in MDCK-II cells. Interestingly, we discovered that, in both 2D and 3D cultures, the formation of the apical cell cortex begins with the fusion of large intracellular apical precursor organelles called vacuolar apical compartments (VACs) at developing cell-cell junctions. Our time-resolved proteomics and imaging analyses revealed a dynamic protein network that likely coordinates the exocytosis of VACs and lumen initiation with the formation and maturation of the AJC. Furthermore, we report that loss of the Crumbs complex proteins Pals1 or PatJ or inhibition of Rho/ROCK signaling impedes VAC exocytosis at the AMIS, resulting in severe defects in lumen morphogenesis. Overall, our findings define a molecular network for de novo cell polarization and highlight Pals1/PatJ as key regulators of apical domain initiation. We further propose that VACs represent a previously unrecognized transport carrier that plays a crucial role in the rapid establishment of apical domain identity.