Bouea macrophylla Griff is a member of the Anacardiaceae family, which has edible fruits. Due to the high nutritional value, appealing taste, and attractive color, the fruit juice of B. macrophylla has the potential to be developed as a functional beverage. The present study was conducted to determine the phytochemical profile of B. macrophylla fruit juice using GC-MS and LC-MS/MS. GC-MS analysis was performed with the Agilent Technologies 7890 Gas Chromatograph with automated sampling and tandem Agilent 5975 Mass Selective Detector and peak analysis with the Chemistation data system. LC-MS/MS QTOF analysis was performed with UPLC Waters I Class and tandem MS/MS Xevo G2S QTOF with UNIFI software. GC-MS analysis identified five compounds with a quality match of 90% and above, namely 3-pentadecylphenol (31.68%), 5,5’-(oxybis(methylene)]-bis-2-furancarboxy-aldehyde (5.67%), 5-(hydroxymethyl)-2-furancarboxy-aldehyde (23.51%), 4H-pyran-4-one, 2,3-dihydro-3,5-dihydro-6-methyl (5.00%), and n-hexadecanoic acid (4.71%). Five major compounds were identified for the first time in B. macrophylla fruit juice by LC-MS/MS analysis, i.e., (E)-hexadecyl-ferulate, digupigan A, eburicoic acid, hydroginkgolinic acid, and terminalic acid. The health benefit of some of these detected phytochemicals supports the use of juice as the main ingredient for functional food.