The WRKY transcription factor family includes plant-specific transcription factors that are widely involved in plant biotic and abiotic stress responses, growth and development. Tartary buckwheat is a type of small grain with strong resistance to adverse growing conditions. No systematic exploration of the WRKY family in Tartary buckwheat has yet been reported. In this paper, we report the FtWRKY46 gene from Tartary buckwheat and study its role in salt tolerance. FtWRKY46 has transcriptional activation activity in yeast, and FtWRKY46 fused to yellow fluorescent protein localizes to the nucleus. Further studies have found that its transcriptional activation region is located at the N-terminus. A yeast one-hybrid assay indicated that FtWRKY46 could bind to a W-box and activate reporter gene expression. Similarly, transient cotransfection showed that FtWRKY46 could specifically bind to W-box regions and activate reporter gene expression in plants. Furthermore, ectopic expression of FtWRKY46 could enhance Arabidopsis tolerance to salt stress. More specifically, the seed germination rate, root length, chlorophyll content and proline content were significantly higher in transgenic plants ectopically expressing FtWRKY46 than in WT plants after salt stress (P < 0.05), while MDA levels were significantly lower than in WT plants (P < 0.05). Additionally, salt treatment increased the expression of stress-related genes. To summarize, our results suggest that ectopic expression of FtWRKY46 enhance the stress tolerance of transgenic plants by modulating ROS clearance and stress-related gene expression.