Tartary buckwheat (Fagopyrum tataricum Gaertn.) contains high concentration of flavonoids, which are mainly represented by rutin, anthocyanins, and proanthocyanidins. WD40 transcription factors (TFs) play significant roles in the transcriptional regulation of the anthocyanin biosynthetic pathway. In this study, a WD40-repeat protein gene (designated as FtWD40) was identified and characterized from tartary buckwheat. The bioinformatics analyses showed that the putative FtWD40 shared a high level of similarity with MtWD40-1, which is a positive regulator in anthocyanin biosynthesis of Medicago truncatula. The yeast one-hybrid assay indicated that FtWD40 had transcriptional activation activities. During florescence, FtWD40 was highly expressed in flowers compared to other organs. Furthermore, its overexpression in tobacco resulted in a remarkable deepening of petal pigmentation in flowers due to a significant increase in anthocyanins accumulation. Meanwhile, the expression of dihydroflavonol-4-reductase (DFR) and anthocyanin synthase (ANS) was upregulated 1.95- and 1.56-fold, respectively. In contrast, the expression level was lower for flavonol synthase (FLS) in the transgenic lines. To the best of our knowledge, this is the first functional characterization of a WD40 transcription factor (FtWD40) from tartary buckwheat that controls the anthocyanin pathway.