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One previously undescribed alkaloid, named penifuranone A (<b>1</b>), and three known compounds (<b>2</b>–<b>4</b>) were isolated from the mangrove endophytic fungus <i>Penicillium crustosum</i> SCNU-F0006. The structure of the new alkaloid (<b>1</b>) was elucidated based on extensive spectroscopic data analysis and single-crystal X-ray diffraction analysis. Four natural isolates and one new synthetic derivative of penifuranone A, compound <b>1a</b>, were screened for their antimicrobial, antioxidant, and anti-inflammatory activities. Bioassays revealed that penifuranone A (<b>1</b>) exhibited strong anti-inflammatory activity in vitro by inhibiting nitric oxide (NO) production in lipopolysaccharide-activated RAW264.7 cells with an IC₅₀ value of 42.2 μM. The docking study revealed that compound <b>1</b> exhibited an ideal fit within the active site of the murine inducible nitric oxide synthase (iNOS), establishing characteristic hydrogen bonds.