Background/Objectives: Catha edulis, commonly known as khat, is used for its psychoactive effects and is considered a natural amphetamine. The current study investigated the metabolomic profile in the cerebellum of mice after repeated exposure to khat and evaluated the effects of clavulanic acid on the metabolomic profile in the cerebellum in khat-treated mice. Methods: Male C67BL/6 mice that were 6–9 weeks old were recruited and divided into three groups: the control group was treated with 0.9% normal saline for 17 days; the khat group was given khat extract at a dose of 360 mg/kg via the intraperitoneal (i.p) route for 17 days; and another khat group was treated with khat for 17 days and clavulanic acid at a dose of 5 mg/kg for the last 7 days (days 11–17). At the end of the 17th day, the animals were sacrificed, and their brains were immediately collected and stored at −80 °C. The cerebellum region of the brain was isolated in each group by micropuncture using cryostat and underwent a metabolomics study via Gas Chromatography/Mass Spectroscopy (GC/MS). The total peak area ratios of the selected metabolites in the cerebellum after repeated exposure to the khat extract were significantly reduced (p < 0.05) and treatment of the khat group with clavulanic acid significantly increased (all p < 0.05) the total peak areas ratios of the selected metabolites when compared to their corresponding areas in the alternative khat group. These levels of selected metabolites were further confirmed by observing the metabolite peak area ratios and performing a heat map analysis and a principal compartment analysis of the samples in the cerebellum. Results: A network analysis of altered metabolites in the cerebellum showed a strong correlation between the different metabolites, which showed that an increase in one metabolite can modulate the levels of others. An analysis using the MetaboAnalyst software revealed the involvement of selected altered metabolites like lactic acid in many signaling pathways, like gluconeogenesis, while enrichment analysis data showed altered pathways for pyruvate metabolism and disease pathogenesis. Finally, a network analysis showed that selected metabolites were linked with other metabolites, indicating drug–drug interactions. Conclusions: The present study showed that repeated exposure of mice to khat altered the levels of various metabolites in the cerebellum which are involved in the pathogenesis of different diseases, signaling pathways, and interactions with the pharmacokinetic profile of other therapeutic drugs. The treatment of khat-treated mice with clavulanic acid positively modified the metabolomics profile in the cerebellum and increased the levels of the altered metabolites.