The objectives of this research were to investigate urinary metabolome modifications and discover potential intake biomarkers in young women after cranberry juice consumption. Fifteen female college students were given either cranberry juice or apple juice for three days using a cross-over design. Urine samples were collected before and after juice consumption. The metabolome in the urine was analyzed using UHPLC-Q-orbitrap-HRMS-based metabolomics followed by orthogonal partial least squares-discriminant analyses (OPLS-DA). An S-plot was used to identify discriminant metabolites. Validated OPLS-DA analyses showed that cranberry juice consumption significantly altered the urinary metabolome. Compared to the baseline urine or urine after apple juice consumption, cranberry juice consumption increased urinary excretion of both exogenous and endogenous metabolites. The tentatively identified exogenous metabolites included quinic acid, coumaric acid, 4-hydroxy-5-(hydroxyphenyl)-valeric acid-O-sulphate, 5-(dihydroxyphenyl)-P-valerolactone sulfate, diphenol glucuronide, 3,4-dihydroxyphenyl propionic acid, 3-(hydroxyphenyl) propionic acid, 4-O-methylgallic acid, trihydroxybenzoic acid and 1,3,5-trimethoxybenzene. Modifications of endogenous metabolites after cranberry juice consumption included the increases in homocitric acid, hippuric acid, 3-hydroxy-3-carboxymethyl-adipic acid, (2)3-isopropylmalate, pimelic acid and N-acetyl-L-glutamate 5-semialdehyde. These metabolites may serve as urinary biomarkers of cranberry juice consumption and contribute to the bioactivities of cranberries against urinary tract infection.