Momordica charantia (MC) is a climber belongs to the Cucurbitaceae family. While there are accumulating evidences showing its pharmacological activities, the effects of fractionation and processing on its anti-inflammatory activity have not been fully elucidated. In this study, we aimed to investigate the anti-inflammatory effects of MC raw juice and fractions from MC fruit extract and to evaluate the effect of processing methods on its anti-inflammatory activity. First, MC juice was extracted using a conventional juicer (raw juice) and fractionated using a solid phase extraction method into five fractions; strong acid, weak acid, neutral, weak base, and strong base fractions. The raw juice and its fractions then were tested for their anti-inflammatory activities including cyclooxygenase-1 (COX-1), cyclooxygenase-2 (COX-2), 5-lipoxygenase (5-LOX), and 15-lipoxygenase (15-LOX) inhibition assays. The results showed that the COX-1 inhibition activity of MC can be attributed to the neutral metabolites (52.60% inhibition). In contrast, the anti-COX-2 activity of MC was found exerted collectively by metabolites in multiple fractions (strong base, neutral, strong acid fractions). Contrarily, metabolites from all five fractions contributed to the MC inhibition activities on 5-LOX (55.51% inhibition for raw juice) and 15-LOX (55.3% inhibition for raw juice). Additionally, the current findings showed that the juice processing technique influenced the plant bioactivity, where juice extract obtained from slow juicer showed consistently higher anti-inflammatory activities than juice from conventional juicer. In summary, the current study provided evidences of anti-inflammatory action of MC and its fractions, which may contribute towards an improved processing and fractionation strategy.