In wheat (Triticum aestivum L.), Fusarium head blight (FHB) resistance is an important breeding target to reduce yield losses and mycotoxin contamination. We hypothesized that cleistogamous (CL, closed flowering) cultivars have a lower risk of FHB infection than chasmogamous (CH, opened flowering) cultivars because FHB infection usually occurs in the inside of florets or extracted anthers and FHB resistance in CL cultivars decreases mycotoxin accumulation. To test these hypotheses, we produced 126 recombinant inbred lines (RILs) derived from a cross between common wheat varieties ‘U24’ (CL variety) and ‘Saikai 165’ (CH variety). Although ‘U24’ and ‘Saikai 165’ are both resistant to FHB infection, ‘U24’ is susceptible to FHB spread, grain deterioration, and mycotoxin accumulation compared with ‘Saikai 165’. Among the RILs, there were significant differences in all of the tested traits. Although the CL RILs showed less initial FHB infection than CH RILs, there were no significant differences in grain deterioration and mycotoxin accumulation between the 2 groups. An FHB-resistant quantitative trait locus (QTL) located on chromosome 3BS increased resistance to FHB spread, grain deterioration, and mycotoxin accumulation; however, not all CL RILs with this QTL accumulated less mycotoxin than ‘Saikai 165’.