Pollen has an extraordinary ability to convert from a dry state to an extremely rapidly growing state. During pollination, pollen receives water and Ca2+ from the contacting pistil, which will be a directional cue for pollen tube germination. The subsequent rapid activation of directional vesicular transport must support the pollen tube growth, but the molecular mechanism leading to this process is largely unknown. We established a luciferase-based pollination assay to screen genetic mutants defective in the early stage after pollination. We identified a plant-specific VPS13, Arabidopsis thaliana VPS13a as important for pollen germination, and studied its molecular function. AtVPS13a mutation severely affected pollen germination and lipid droplet discharge from the rough endoplasmic reticulum. Cellular accumulation patterns of AtVPS13a and a secretory vesicle marker were synchronized at the polarized site, with a slight delay to the local Ca2+ elevation. We found a brief Ca2+ spike after initiation of pollen hydration, which may be related to the directional cues for pollen tube emergence. Although this Ca2+ dynamics after pollination was unaffected by the absence of AtVPS13a, the mutant suffered reduced cell wall deposition during pollen germination. AtVPS13a mediates pollen polarization, by regulating proper directional vesicular transport following Ca2+ signaling for directional tube outgrowth.