Quercetin is a flavonol polyphenol widely found in many vegetables, grains, and fruits. Quercetin has been shown to inhibit proliferation and invasion of various glioma cells and is regarded as a potential anticancer agent against glioma. However, whether and how this drug could affect brain blood vessels and endothelial cells (EC) are less understood. Further, there is hitherto no report on how quercetin affects brain EC Ca2+ homeostasis. In this report, we investigated the effects of quercetin on Ca2+ homeostasis in mouse brain bEnd.3 EC. We demonstrated that quercetin raised cytosolic Ca2+ level in a concentration-dependent manner. Quercetin-triggered Ca2+ signal composed of both internal Ca2+ release and extracellular Ca2+ influx. Quercetin caused Ca2+ release from the endoplasmic reticulum, and consistently, inhibition of inositol 1,4,5-trisphosphate receptor (IP3R) by xestospongin C (XeC) suppressed quercetin-triggered Ca2+ release. Quercetin also caused Ca2+ release from lysosomes, an observation in concordance with the inhibition of quercetin-triggered Ca2+ release by trans-Ned-19, a blocker of two-pore channels. As quercetin depleted intracellular Ca2+ storage, it suppressed ATP-induced Ca2+ release and thereby blunted ATP-triggered Ca2+ signaling. In addition, quercetin co-treatment significantly suppressed ATP-stimulated nitric oxide release. Our work therefore showed, for the first time, quercetin perturbed intracellular Ca2+ stores and strongly suppressed ATP-triggered response in bEnd.3 cells.