The long-term survival of alfalfa (Medicago sativa L.) is limited by several factors, including Fusarium root rot (FRR) caused by several Fusarium species. Resistance to FRR in alfalfa is usually evaluated under field conditions or in a soil culture test conducted under greenhouse conditions in artificially inoculated soil, both of which involve the assessment of a disease severity index. A new hydroponics screening (HS) method was developed to more efficiently screen a large population of alfalfa germplasm for resistance to FRR. Spearman correlation analysis revealed that in terms of disease severity index (r = 0.94) and disease incidence (r = 0.86), the results obtained with the HS-method were correlated strongly with the soil culture test, indicating the effectiveness of this new method. The time needed for screening with the HS method was shortened to 28 days compared with 125 days for the soil culture test. Thus, it is feasible to apply the new method at an early stage of alfalfa growth, which enables several cycles of selection each year. Moreover, the space requirements for the HS method were one-fifth of those of the soil culture test. The HS method is an efficient tool for alfalfa researchers to identify FRR-resistant alfalfa genotypes, especially in a large breeding population at early evaluation stages. This method could be adapted for the screening of other plant species for resistance to Fusarium spp. or other root pathogens.