Quinoa saponins are pentacyclic triterpene compounds composed of one triterpenoid glycoside and two different sugar chains. Previous studies have showed that natural quinoa saponins showed little or no antifungal activity, and there are few reports about their antifungal effects in recent decades. Fusarium wilt caused by Fusarium oxysporum f. sp. lycopersici (FOL) is the most serious for tomatoes in the field and under greenhouse conditions. The main objective of this study was to investigate the effectiveness of different concentrations and application modes of crude saponins from quinoa bran against the causal pathogen of tomato wilt under a greenhouse experiment. The results showed that the anti-FOL activity of quinoa saponins was weak in vitro, but significantly enhanced in vivo. Tomato seeds and seedlings treated with solution of quinoa saponins at 0.5 and 1.0 g/L significantly reduced the disease incidence (%) of tomato Fusarium wilt. The treatment types of saponin solution have influence on the preventive effects (%) of tomato seedlings against Fusarium wilt, among them, root soaking > foliar spray > seed soaking. The treatment of seed soaking with quinoa saponins inhibited germination of tomato seeds to some extent. However, the germination rate of tomato seeds after saponin soaking was comparable to the chemical pesticide (thiram carboxin); therefore, it could be used to control tomato wilt disease. This is due to the fact that the antifungal activity of quinoa saponins in vivo was much higher than that in vitro when the saponin concentration was between 0.5–1.0 g/L, indicating that the antifungal activity of quinoa saponins may be achieved mainly by inducing resistance. This investigation supports the potential use of quinoa saponins as a supplier of antifungal compounds, and could be the foundation for a future study examining the use of quinoa bran as a new resource against FOL.