This study was to examine the effects of four fungal polysaccharides, namely exo-polysaccharide (EPS), water-extracted mycelia polysaccharide (WPS), sodium hydroxideextracted mycelia polysaccharide (SPS), and hydrochloric-extracted mycelia polysaccharide (APS) obtained from the endophytic fungus Bionectra pityrodes Fat6, on the sprout growth and flavonoids production of Fagopyrum tataricum. Without obvious changes in the appearance of the sprouts, the exogenous polysaccharide elicitors notably stimulated the sprout growth and functional metabolites accumulation, and the stimulation effect was mainly depended on the polysaccharide species along with its treatment dose. With application of 150 mg/l of EPS, 150 mg/l of WPS and 200 mg/l of SPS, the total rutin and quercetin yield of buckwheat sprouts was effectively increased to 49.18 mg/(100 sprouts), 50.54 mg/(100 sprouts), and 52.27 mg/(100 sprouts), respectively. That was about 1.57- to 1.66-fold in comparison with the control culture of 31.40 mg/(100 sprouts). Moreover, the present study revealed the accumulation of bioactive flavonoids resulted from the stimulation of the phenylpropanoid pathway by fungal polysaccharide treatments. It could be an efficient strategy for improving the nutritional and functional quality of tartary buckwheat sprouts applied with specific fungal elicitors.