Prunella vulgaris, an essential component of traditional Chinese medicine, is suitable for growing in soil with a pH value ranging from 6.5 to 7.5. However, it is primarily cultivated in acidic soil regions of China, where its growth is frequently compromised by acidic stress. Selenium (Se) has been recognized for its potential to enhance stress tolerance in plants. However, its role in acid-stress-induced oxidative stress is not clear. In this study, the effects of varying Se concentrations on the growth and quality of P. vulgaris under acidic stress were investigated. The results showed that acid stress enhanced antioxidant enzyme activities, non-enzymatic antioxidant substances, and osmolyte content, accompanied by an increase in oxidant production and membrane damage. Furthermore, it decreased the photosynthetic capacity, inhibited root and shoot growth, and diminished the yield of P. vulgaris. In contrast, exogenous application of Se, particularly at 5 mg L−1, markedly ameliorated these adverse effects. Compared to acid-stressed plants, 5 mg L−1 Se treatment enhanced superoxide dismutase, peroxidase, ascorbate peroxidase, and glutathione peroxidase activities by 150.19%, 54.94%, 43.43%, and 45.55%, respectively. Additionally, soluble protein, soluble sugar, and proline contents increased by 11.75%, 23.32%, and 40.39%, respectively. Se application also improved root architecture and alleviated membrane damage by reducing hydrogen peroxide, superoxide anion, malondialdehyde, and electrolyte leakage levels. Furthermore, it significantly enhanced the photosynthetic capacity by elevating pigment levels, the performance of PSI and PSII, electron transfer, and the coordination of PSI and PSII. Consequently, plant growth and spica weight were significantly promoted, with a 12.50% increase in yield. Moreover, Se application upregulated key genes involved in flavonoid and phenolic acid metabolic pathways, leading to elevated levels of total flavonoids, caffeic acid, ferulic acid, rosmarinic acid, and hyperoside by 31.03%, 22.37%, 40.78%, 15.11%, and 20.84%, respectively, compared to acid-stressed plants. In conclusion, exogenous Se effectively alleviated the adverse effects of acid stress by improving the antioxidant system, growth, and photosynthetic capacity under acid stress, thus enhancing the yield and quality of P. vulgaris.