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Nephelium lappaceum (rambutan) is an edible tropical fruit that is widely grown in Southeast Asia. In general, the seeds contain high nutrients, but rambutan seeds are thrown out during processing. In this study, the anti-aging activity of rambutan seeds was evaluated with a new approach through the selective inhibition of the senescence-associated secretory phenotype (senomorphics). Luciferase promoter assays using p16INK4A and SA-β-gal promoters for rambutan showed that its seeds possessed strong senomorphic activity. Molecular networking using ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-qTOF-MS) with a tandem database (UPLC-qTOF-MS/MS) was applied to determine the chemical composition of rambutan. Based on the activity results, nine compounds, one new (7) and eight known kaempferol type compounds, were isolated from the seeds. Compounds 2, 4 and 9 significantly reduced the mRNA expression levels of senescence markers, such as p16INK4A, p21CIP1, p53 and SA-β-gal. These compounds also significantly increased the level of SIRT1, a longevity modulator. Compounds 2, 4 and 9 decreased the mRNA expression levels of senescence-associated secretory phenotypes (SASPs) and subsequently decreased the number of SA-β-gal-positive cells. Thus, rambutan seeds and its constituents might be able to protect against age-related problems.