The environmental accumulation of polycyclic aromatic hydrocarbons (PAHs), such as benzo(a)pyrene (BaP), poses significant threats to ecosystems and public health due to their persistent nature, mutagenic potential, and well-documented carcinogenicity. In this study, we investigated the ability of the extremophilic yeast Debaryomyces hansenii to activate specialized detoxification mechanisms for BaP degradation, even under nutrient-deprived conditions. When exposed to 100 ppm BaP, D. hansenii eliminated over 70% of the contaminant within 3 days, while maintaining normal growth dynamics. RNA-Seq analysis revealed widespread transcriptional remodeling, with 1,179 genes upregulated and 1,031 downregulated under BaP-only conditions, and 1,067 upregulated and 977 downregulated genes during cometabolic exposure (2% glucose + 100 ppm BaP), from a total of 6,506 annotated genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses highlighted the activation of xenobiotic degradation pathways, notably involving cytochrome P450 monooxygenases, epoxide hydrolases, and glutathione S-transferases, alongside an enhanced antioxidant response and finely tuned glutathione homeostasis. This work presents the transcriptomic profile of BaP detoxification in D. hansenii, which reveals a complex transcriptional activation of genes related to stress adaptation and detoxification. Collectively, these findings suggest that D. hansenii could represent a promising eukaryotic platform for bioremediation.