Endogenous sinapic acid (SA), sinapine (SP), sinapoyl glucose (SG) and canolol (CAN) of canola and mustard seeds are the potent antioxidants in various lipid-containing systems. The study investigated these phenolic antioxidants using different fractions of canola and mustard seeds. Phenolic compounds were extracted from whole seeds and their fractions: hulls and cotyledons, using 70% methanol by the ultrasonication method and quantified using HPLC-DAD. The major phenolics from both hulls and cotyledons extracts were SP, with small amounts of SG, and SA with a significant difference of phenolic contents between the two seed fractions. Cotyledons showed relatively high content of SP, SA, SG and total phenolics in comparison to hulls (p < 0.001). The concentration of SP in different fractions ranged from 1.15 ± 0.07 to 12.20 ± 1.16 mg/g and followed a decreasing trend- canola cotyledons > mustard cotyledons > mustard seeds > canola seeds > mustard hulls > canola hulls. UPLC-tandem Mass Spectrometry confirmed the presence of sinapates and its fragmentation in these extracts. Further, a high degree of correlation (r = 0.93) was noted between DPPH scavenging activity and total phenolic content.