Background: Scutebarbatine A is a new neo-Clerodane Diterpenoid Alkaloids from Scutellaria barbata, which has many pharmacological effects, such as anti-tumor, antibacterial, and anti-inflammatory. However, there are no studies on the metabolism of Scutebarbatine A. Objective: The objective of this study is to explore the metabolism of Scutebarbatine A in the body, the bile, plasma, urine, and feces samples of rats after administration were investigated. Methods: The biological samples were investigated using ultra-high-performance liquid chromatography coupled with Q Exactive hybrid quadrupole-orbitrap high-resolution mass spectrometry (UPLC-Q-Orbitrap-HRMS). Results: A total of 20 metabolites were identified: 16 phase I metabolites and 4 phase II metabolites. The main metabolic pathways were hydrolysis, oxidation, hydrogenation, dehydration, and combination with sulfate. Conclusion: This study further elucidates the metabolism of Scutebarbatine A in rats and provides a reference for the study of its pharmacodynamic material basis and pharmacological mechanism.