Whole wheat flour possesses many nutritional properties because of its abundant bioactive components which are affected by cultivar, but little attention is paid to its relationship with storage conditions. In this study, phenolic extracts of whole wheat flour from four cultivars stored under different conditions (aerated and under vacuum) and different times (0, 2, 4, 8 weeks) were obtained. The total polyphenol (TPC) and flavonoid (TFC) contents, composition of phenolic acids, and antioxidant activities (AA) of phenolic extracts were evaluated. The results showed that Verna exhibited the highest levels of TPC, TFC, and AA for both storage conditions among the four cultivars. Moisture content, TFC, and AA fluctuated during storage. After 8 weeks, the TPC, TFC, and AA decreased with respect to Week 0 in all the cultivars. The TPC losses ranged between 16.39% and 20.88% and TFC losses from 14.08% to 31.18%. The AA losses were approximately 30% from the DPPH assay, but no significant losses were shown in the FRAP assay. However, these parameters were not distinctive between the two storage conditions. The wheat phenolic acid profiles were influenced more by storage time than storage conditions in all cultivars. Overall, the results validate the effect of the storage time on wheat polyphenol.