Sweet corn is susceptible to the attack of various pathogens that affect its metabolism and compromise its quality and production. This study aimed to identify the causal agent of stem rot in sweet corn plants under greenhouse conditions. The identity of the pathogenic isolate was confirmed by sequencing of internal transcribed spacer (ITS1/ITS4), beta-tubulin (BT2A/BT2B), calmodulin (CL1/CL2) and translation elongation factor 1α (TEF1). The morphological and sequencing characteristics showed that Fusarium sacchari, which belongs to the Fusarium fujikuroi complex, is directly associated with the symptoms observed in the field. This fungal isolate has never been associated with diseases in Zea mays (saccharata group) in Brazil; therefore, this is the first report of the fungus infecting sweet corn in a cultivated area.