Although non-aflatoxigenic Aspergillus flavus strains have been thoroughly used to reduce aflatoxin contaminations in maize and nuts, the biocontrol potential of these strains for the management of fungal pathogens remains almost unexplored. This study aimed to evaluate the biocontrol mechanisms and efficacy of A. flavus NJC04, which was previously isolated from kiwifruit, for the control of soybean pathogen Sclerotinia sclerotiorum. Non-aflatoxigenic NJC04 was shown to contain important deletions in the aflatoxin and cyclopiazonic acid biosyntheses. Interestingly, this strain inhibited mycelial growth and sclerotia formation of soybean pathogen Sclerotinia sclerotiorum. NJC04 showed various antifungal mechanisms against S. sclerotiorum, including competition for space and nutrients, and the production of antifungal kojic acid, which was detected at 87 ± 4 mg/L in the culture medium. NJC04 colonized soybean plants during long periods and did not cause necrotic lesions. Preventive application of 1 × 107 and 1 × 108 NJC04 spores/mL reduced Sclerotinia rot symptoms by 83.2 % and 100 %, respectively. Collectively, the biocontrol efficacy of non-aflatoxigenic NJC04 for the control of S. sclerotiorum was examined for the first time revealing new insights into the mechanisms used by A. flavus strains to compete with plant fungal pathogens.