There is a huge demand for novel anticancer agents with fewer side effects compared to current therapies. Pitaya, or dragon fruit, is a reservoir of potent anticancer compounds. This research aimed to analyze the phytochemical components of pulp and peel extracts using LC-MS and GC-MS, and to investigate the in vitro effects of both extracts against cancer (breast, MCF-7, and colon, Caco-2) and normal (lung; WI-38 and breast; MCF-10A) cell proliferation using the MTT assay. The apoptosis potential of the anticancer effects was also evaluated using flow cytometry, RT-PCR, and Western blot. The total phenolic and flavonoid contents in the peel extract were significantly higher than those in the pulp extract. Compared to the flavonoid and phenolic acid standards, the LC-MS analysis revealed the presence of nine compounds, which were represented as 84.32 and 5.29 µg/g of the flavonoids and 686.11 and 148.72 µg/g of the phenolic acids in the peel and pulp extracts, respectively. Among the identified compounds, chlorogenic acid, caffeic acid, ferulic acid, and rutin were found at the highest concentration in both plant extracts. Both extracts displayed cytotoxic activity against MCF-7 and Caco-2 cancer cells after 48 h of treatment at IC values ranging from 14 to 53 μg/mL with high selective indices against normal WI-38 and MCF-10A cell lines. The increase in apoptosis was revealed by the overexpression of p53, BAX, and caspase-9 and the downregulation of antiapoptotic Bcl-2 mRNA and protein expressions. The results indicate that extracts can be a plant source for cancer therapy.