Capsaicin (CAP), a crucial compound found in chili peppers, not only contributes to their spicy flavor but also possesses several industrial applications. CAP biosynthetic pathway is well known, while its transport mechanism remains elusive. Herein, we performed a comparative transcriptome analysis conducted on pepper fruit tissues at three different stages of development. Four important CAP transporter genes, including one MATE and three ABCs, were identified by differential expression and WGCNA analysis. Specifically, the expression patterns of three ABC genes were assessed in the septum of fruits from nine distinct genotypes of peppers with high capsaicin levels. Interestingly, CaABCG14 was associated with variations in CAP concentration and co-expressed with genes involved in CAP biosynthesis. Transient expression assay revealed that CaABCG14 is localized to the membrane and nucleus. Silencing of CaABCG14 resulted in a notable reduction in the levels of CAP contents and the expression of its biosynthetic genes in the septum of pepper. The overexpression of CaABCG14 greatly intensified the cytotoxic effects of CAP on the yeast cells. Taken together, we for the first time identified a new transporter gene CaABCG14, regulating the CAP accumulation in pepper septum. These findings offer a fresh molecular theoretical framework for CAP transport and accumulation.