Rice bakanae disease caused by Fusarium fujikuroi is one of the most famous seed borne diseases. If infected seeds are used, this disease will occur with serious impacts. Thus, a simple, reliable, specific and sensitive method for surveillance is urgently needed to screen infected seeds and seedlings at early developmental stages. In this study, a rapid and efficient loop-mediated isothermal amplification (LAMP) method was developed to detect F. fujikuroi in contaminated rice seeds and seedlings for diagnosis of bakanae disease. NRPS31 gene plays an important role in the gibberellic acid (GA) bio-synthesis of F. fujikuroi, and is not present in any other sequenced fungal genome, and thus was adopted as the target for LAMP primer design. The LAMP assay enables the fast detection of as little as 1 fg of pure genomic F. fujikuroi DNA within 60 minutes. Further tests indicated that the LAMP assay was more sensitive and faster than the traditional isolation method for F. fujikuroi detection in rice seeds and seedlings. Our results show that this LAMP assay is a useful and convenient tool for detecting F. fujikuroi, and it can be applied widely in seed quarantine of bakanae disease, providing valid data for disease prevention.