BACKGROUND: Excessive activation of microglia triggers pro-inflammatory responses, exacerbating neuronal damage and accelerating the progression of Alzheimer's disease (AD). Thus, targeting abnormal microglial activation represents a promising therapeutic strategy for AD. In this study, we identified sclareol (SCL) through compound library screening as a potent anti-inflammatory agent capable of crossing the blood-brain barrier. However, there are currently no reports on whether SCL modulates microglial inflammation or ameliorates AD pathology. OBJECTIVE: To evaluate the anti-inflammatory effects and underlying molecular mechanism of SCL on microglial-mediated inflammation and neuronal damage in AD. METHODS: Drug Affinity Responsive Target Stability (DARTS), Liquid Chromatography-Tandem Mass Spectrometry (LC-MS), protein interaction assays, Biolayer Interferometry (BLI), and molecular docking were used to explore the interaction between SCL and cyclin-dependent kinase 9 (CDK9). Behavioral tests and immunofluorescent (IF) staining were performed to assess the effects of SCL on microglial activation and AD pathology. The molecular mechanism of the anti-inflammatory effect of SCL was analyzed by interfering with CDK9. RESULTS: SCL significantly inhibited the release of proinflammatory mediators, reduced neuronal damage, and alleviated cognitive deficits in AD model mice. Notably, SCL demonstrated the ability to cross the blood-brain barrier (BBB), highlighting its therapeutic potential. Mechanistically, SCL binds directly to CDK9, which contributes to the inflammatory response through its interaction with NF-κB. Knockdown of CDK9 reduced the NF-κB-mediated inflammatory response, but did not have an additive effect on SCL, indicating that SCL's efficacy is mediated by CDK9 inhibition and subsequent suppression of the NF-κB signaling pathway. CONCLUSION: This study demonstrates that SCL exerts neuroprotective effects in AD mice by targeting CDK9 and downstream NF-κB signaling pathway to reduce the inflammatory activation of microglia. These findings suggest that SCL is a promising candidate for the treatment of AD, offering a novel therapeutic approach to mitigate disease progression through modulation of microglial activation.