Stelechocarpus burahol (kepel) is valued for its aromatic fruits and medicinal leaves, yet its genomic and phytochemical features remain poorly characterized. This study estimated the nuclear DNA content of kepel leaves at 3.96 pg per haploid genome (genome size: 3873 Mbp) and comprehensively profiled their bioactive metabolites. Leaf extracts prepared with water and 70% ethanol, with or without pulsed electric field (PEF) treatment, were analyzed using HPLC-MS, UHPLC-QTOF-MS, HPLC-DAD, and GC-MS. Leaf extracts showed the highest phenolic and flavonoid contents, with PEF markedly improving ethanolic extraction efficiency. A total of 72 phenolics, 2 tocopherols, 3 tocotrienols, and several novel vitamin E derivatives were detected, alongside abundant catechins, tannic acid, and gallic acid. PEF significantly enhanced catechin recovery: catechin (C) increased from 153.7 to 846.8 mg/g and epicatechin (EC) from 338.2 to 921.4 mg/g in water extracts, while ethanolic extracts rose from 335.3 to 905.1 mg/g (C) and 245.0 to 616.9 mg/g (EC). Epigallocatechin 3-gallate (EGCG), absent in untreated leaves, reached 799.9 mg/g in water and 231.9 mg/g in ethanol extracts after PEF. In fruits, PEF reduced phenolic recovery in water extracts (C: 236.7 → 136.8 mg/g; EC: 135.4 → 118.2 mg/g; EGCG: 2892.2 mg/g → undetectable),
but slightly improved ethanolic extracts (C: 237.8 → 289.4 mg/g). GC-MS identified
19 volatile compounds contributing to the fruit’s aroma. This work provides the first integrated report of kepel genome size and phytochemical composition, highlighting PEF as a promising strategy to enhance leaf catechin extraction and supporting kepel’s potential as a functional food and medicinal resource.