The purpose of this study was to investigate the effects of endophytic fungi from tartary buckwheat on the host sprout growth and functional metabolite production. Without obvious changes in the appearance of the sprouts, the exogenous fungal mycelia elicitors notably stimulated the sprout growth and rutin accumulation, and the stimulation effect was mainly depended on the mycelia elicitor species along with its treatment dose. Three endophytic fungi Fat6 (Bionectria pityrodes), Fat9 (Fusarium oxysporum) and Fat15 (Alternaria sp.) were screened to be the most effective candidates for promoting F. tataricum sprout growth and rutin production. With application of polysaccharide (PS, 150 mg/l) of endophyte Fat6, PS (200 mg/l) of endophyte Fat9, and PS (150 mg/l) of endophyte Fat15, the rutin yield was effectively increased to 47.89 mg/(100 sprouts), 45.85 mg/(100 sprouts) and 46.83 mg/(100 sprouts), respectively. That was about 1.5- to 1.6-fold compared to the control culture of 29.37 mg/(100 sprouts). Furthermore, the present study revealed that the biosynthesis of the functional flavonoid resulted from the stimulation of the phenylpropanoid pathway by mycelia polysaccharide treatments. Application of specific fungal elicitors could be an efficient strategy for improving the nutritional and functional quality of tartary buckwheat sprouts.