Polyphenols with antioxidant compounds represent an important group of bioactive substances in apple production. The objectives of this study were firstly to measure four parameters of antioxidant capacity (AC) and polyphenol content (AC-FRAP (Ferric Reducing Ability of Plasma), AC-DPPH (2,2-diphenyl-1-picrylhydrol), AC-TEAC (Trolox Equivalent Antioxidant Capacity) and total polyphenol content (TPC)) of four scab-resistant apple cultivars (‘Fujion’, ‘Gaia’, ‘Isaaq’ and ‘Smeralda’) using six extraction methods (water control, pectinase, two approaches using ethanol (EtOH-1 and EtOH-2), methanol (MetOH) and methanol + acetone (MetOH + Acetone), and secondly to provide intercorrelations between antioxidant and polyphenol contents of the four resistant apple cultivars under the six extraction methods. Analysis of variance on the four parameters showed a significant (p = 0.05) effect for extraction methods and cultivars. TPC showed the highest values among the four parameters in all extraction methods and cultivars compared to the other three measurements. The pectinase extraction method showed the highest TPC values for the four cultivars. The EtOH-2 extraction method showed the lowest AC-FRAP value for all cultivars. The EtOH-2 extraction method showed the highest AC-DPPH values, whereas the control method showed the lowest values for the four cultivars. The AC-TEAC values were generally the lowest, ranging between 10.8 and 40.5 mg TE 100 g−1 dry matter, and they showed various effects on extraction methods and cultivars. Correlation and regression analyses of 36 pair-variables showed that two pair-variables (TPC vs. AC-FRAP and AC-TEAC vs. AC-DPPH) were significant for all of the six extraction methods and for all cultivars. In conclusion, the extraction method using pectinase enzyme provided the most stable yield of polyphenol content from apple flesh, as confirmed by the examination of four scab-resistant apple cultivars.