Fusarium crown rot (FCR) is a significant global issue in wheat production. Planting resistant cultivars is the most effective strategy for mitigating FCR damage. However, breeding for FCR resistance is challenged by the lack of a reliable and high-throughput method for rapid and accurate assessment of numerous genotypes. This study evaluated FCR resistance in 50 wheat genotypes using the common soil-based method. None of the genotypes were immune or highly resistant and only 6.0% (three genotypes) showed moderate resistance at the seedling stage. Resistant and susceptible genotypes were then selected for preliminary experiments. A rapid water-culture method for assessing FCR resistance in wheat seedlings was developed. Seedlings were planted in petri dishes and inoculated by spraying conidial suspensions. This new method, which takes 15 days (about 50% of the time required for soil-based methods), requires minimal space and eliminates variability associated with soil or potting mixes. The disease index correlation between water-culture and soil-based methods was significant (p < 0.01) with a correlation coefficient of 0.901. The resistance evaluation consistency among 50 genotypes using both methods was 94.0%, indicating high reproducibility and strong agreement with soil-based results. Therefore, this new method should be a valuable tool for initial screening of FCR-resistant germplasms from numerous genotypes in breeding programs.