Drought is a severe environmental constraint to plant productivity. Being a multidimensional stress, it triggers a wide variety of plant responses at the physiological, biochemical, and molecular levels. Exploring stress-related genes in endemic plants such as Veronica nakaiana paves the way to identifying how these plants thrive in their respective locations. To identify genes related to the drought stress response in V. nakaiana, we compared the transcriptomes of plants under well-watered (WW) and drought-stressed (DS) conditions using RNA-sequencing. In DS plants, plant height, root length, leaf area, and stomatal width were significantly reduced, and stomatal density was increased. Interestingly, fresh, and dry weights did not significantly differ between WW and DS plants. To our knowledge, this was the first attempt to establish a de novo transcriptome-based sequence assembly of V. nakaiana under drought stress. We identified 2,261 upregulated and 3,315 downregulated differentially expressed genes in DS plants. In-depth data analysis revealed that a large number of these genes were associated with drought stress responses, including heat shock proteins, abiotic stress related transcription factors, and factors involved in abscisic acid signaling, lipid metabolism, and auxin binding. The results provide insights into the different mechanisms contributing to the drought response in V. nakaiana.