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A new pyrazine derivative, trypilepyrazinol (<b>1</b>), a new α-pyrone polyketide, (+)-neocitreoviridin (<b>2</b>), and a new ergostane analogue, 3β-hydroxyergosta-8,14,24(28)-trien-7-one (<b>3</b>), were isolated and characterized along with five known compounds from the marine-derived fungus <i>Penicillium</i> sp. IMB17-046. The structures of these new compounds were determined using spectroscopic data analyses (HRESIMS, 1D- and 2D-NMR), X-ray crystallography analysis, and TDDFT ECD calculation. Compounds <b>1</b> and <b>3</b> exhibited broad-spectrum antiviral activities against different types of viruses, including human immunodeficiency virus (HIV), hepatitis C virus (HCV), and influenza A virus (IAV), with IC₅₀ values ranging from 0.5 to 7.7 μM. Compounds <b>1</b> and <b>2</b> showed antibacterial activities against <i>Helicobacter pylori</i>, a causative pathogen of various gastric diseases, with minimum inhibitory concentration (MIC) values of 1–16 μg/mL.