<p>In this study, we aimed to determine the optimal concentration of selenium (Se) required to increase the bioactive compound content, growth, antioxidant capacity, and photosynthetic parameters in <i>Agastache rugosa.</i> We investigated the effects of various concentrations of Se (0, 2.5, 5, 10, 20, and 40 µmol mol^− 1) on the growth, chlorophyll contents, total carotenoid contents, photosynthetic characteristics, antioxidant enzyme activities, and bioactive compound contents in <i>A. rugosa</i> plants. High Se concentrations, particularly 20 and 40 µmol mol^− 1, significantly enhanced almost all plant growth parameters, including the flower branch number, flower fresh weight (FW), leaf area, stem length, shoot FW, stem FW, root dry weight (DW), flower DW, shoot DW, and overall plant DW. Total chlorophyll and chlorophyll a contents were significantly increased with 20 µmol mol^− 1 Se, and the total carotenoid contents were significantly increased with 5, 10, 20, and 40 µmol mol^− 1 of Se compared to those in the untreated treatment. Additionally, net photosynthetic rate was significantly increased after 20 and 40 µmol mol^− 1 Se treatments. Furthermore, total flavonoid and phenolic contents and antioxidant enzyme activities (superoxide dismutase, 2,2-diphenyl-1-picrylhydrazyl radical-scavenging, peroxidase, and catalase) were significantly elevated after high-concentration Se treatments. Specifically, rosmarinic acid and acacetin 1 contents peaked with 20 µmol mol^− 1 Se, whereas tilianin and acacetin contents were significantly higher in the 10 µmol mol^− 1 Se treatment group than in the untreated group. Acacetin 2 and 3 contents were the highest after 20 µmol mol^− 1 Se treatment. Overall, our findings suggest that Se, particularly at 20 and 40 µmol mol^− 1, positively influences the growth, photosynthetic characteristics, bioactive compound content, and antioxidant enzyme activity in <i>A. rugosa</i> plants, thereby enhancing the plant productivity and quality.</p>