The objective of this study was to determine the proper electrical conductivity (EC) of a nutrient solution (NS) for accumulating bioactive compounds of Agastache rugosa without decreasing plant growth. Six-week-old seedlings were transplanted in a deep flow technique system with Hoagland NS with a 2.0 dS·m−1 EC for the initial week. From eight days after transplanting, the plants were treated with six EC treatments of 0.5, 1.0, 2.0, 4.0, 6.0, and 8.0 dS·m−1 for three weeks. Plant growth parameters, leaf gas exchange parameters, the relative chlorophyll value, and the ratio of variable to maximum fluorescence (Fv/Fm) were measured, and the rosmarinic acid (RA), tilianin, and acacetin concentrations were analyzed at 28 days after transplanting. The results showed that almost all plant growth parameters were maximized at 2.0 and 4.0 dS·m−1 and minimized at 8.0 dS·m−1 compared with the other EC treatments. The relative chlorophyll and Fv/Fm values were maximized at 2.0 and 4.0 dS·m−1. Similarly, leaf gas exchange parameters were increased at 2.0 and 4.0 dS·m−1. The RA content exhibited significantly higher values at 0.5, 1.0, 2.0, and 4.0 dS·m−1 compared with other treatments. The tilianin and acacetin contents exhibited the significantly highest values at 4.0 and 0.5 dS·m−1, respectively. These results suggest optimal EC treatment at 4.0 dS·m−1 for increasing bioactive compounds in A. rugosa plants without decreasing plant growth. Excessively high or low EC induced salinity stress or nutrient deficiency, respectively. Furthermore, among the plant organs, the roots of A. rugosa contained the highest RA concentration and the flowers contained the highest tilianin and acacetin concentrations, which revealed a higher utilization potential of the roots and flowers for bioactive compounds.