Drought resistance traits are important for resistance to preharvest aflatoxin contamination in peanut seeds caused by Aspergillus flavus; however, the evidence has been controversial. The problem might be solved by investigating fungal activities relevant to drought effects on the early pod. Herein, drought impacts on three peanut cultivars with different genotypes were shown as leaf adaptation to reduce transpiration. High impacts were observed in ICGV 98300, ICGV 98308, and Tainan 9 cultivars. Fungal ingress was not histologically found across sclerenchyma to the inner parenchyma of R3 pod pericarp regardless of genotypes or water conditions. Similar activities occurred in R5 pods of non-drought stressed control plants, and the fungus was not detectable inside newly developing seeds. Healthy sclerenchyma likely displayed a physical barrier role. Drought led to the fungal detection in seeds of the three cultivars. The results corresponded to the fungal germination tests in mature seeds, where A. flavus was found, of stressed plants. A. flavus nor-1 transcript was occasionally detected showing A. flavus colonization in a number of R5 kernels of control plants. Under drought condition, the nor-1 expression was increased by 2.5 folds in Tainan 9 and ICGV 98300, and a small increase was observed in ICGV 98308. The reducing sugar contents in R5 kernels of Tainan 9 and ICGV 98300 were also increased, suggesting the stimulation of oxidative stress and aflatoxin synthesis. High A. flavus virulence, based on nor-1 expression and reducing sugar content, was remarkable in ICGV 98308 under water regimes for control and drought-stressed plants under greenhouse conditions.