Pitaya, commonly known as dragon fruit, has generated considerable consumer interest because of its attractive color and micronutrient content. The present study investigated the total polyphenol and flavonoid content, antioxidant activity against various free radicals, and antiproliferative effect on several cancer cell lines of extracts of flesh and peel of white and red pitayas, collected from Jeju Island, Korea. The total polyphenol and flavonoid contents of 80% methanol extracts of red pitaya peel (RPP) and white pitaya peel (WPP) were approximately 3- and 5-fold higher than those of red pitaya flesh (RPF) and white pitaya flesh (WPF), respectively. Overall, the total flavonoid and polyphenol contents of these extracts were RPP>WPP>RPF>WPF and WPP>RPP>RPF>WPF, respectively. In addition, a study involving nontargeted high-performance liquid chromatography coupled with a photodiode array and electrospray ionization mass spectrometry (HPLC-PDA-ESI-MS) of different pitaya extracts indicated the presence of phenolic, hydroxycinnamic acid derivatives, flavonol glycosides, betacyanin, and its derivatives with a few unknown compounds. Separately, peel extracts of both red and white pitayas showed higher 2,2-diphenyl-1-picrylhydrazyl, hydroxyl, and alkyl radical-scavenging activity than did the corresponding flesh extracts. Both peel extracts also showed stronger antiproliferative activity against AGS and MCF-7 cancer cells than either flesh extract. There was a direct correlation between the phenolic content and antioxidant effect, but no correlation observed between antioxidant activity and antiproliferative activity. These results suggest that the peel of white and red pitaya may be a valuable ingredient in foods and may also be useful in cosmetic, nutraceutical, and pharmaceutical applications.