Orange juice is considered an excellent dietary source of several bioactive compounds with beneficial properties for human health. Citrus sinensis Osbeck cv. 'Cara Cara' is a bud mutation originated from 'Washington' navel orange, also known as 'Bahia' navel orange. The ascorbic acid, flavonoid, and carotenoid contents in pasteurized and nonpasteurized Bahia and Cara Cara juices using two LC-MS/MS platforms were investigated. Higher ascorbic acid content was observed in Bahia compared to Cara Cara in both pasteurized and nonpasteurized juices. Total flavanones content as well as hesperidin levels were higher in Cara Cara with respect to Bahia pasteurized juice. Cara Cara was also characterized by a significantly higher and diversified carotenoid content compared to Bahia juice with a mixture of (Z)-isomers of lycopene, all-E-β-carotene, phytoene, and phytofluene isomers accounting for the highest carotenoid proportion. The exceptionally high carotenoid content of Cara Cara may be particularly interesting for nutritional or functional studies of uncommon carotenes in a citrus food matrix.