Global deterioration of water, air, and soil quality by the release of toxic chemicals from anthropogenic pollutants is becoming a serious global problem. The extensive use of copper oxide nanoparticles (CuO NPs) can be environmentally hazardous when these NPs enter the atmosphere. The present study aimed to evaluate the role of CuO NPs on plant growth, photosynthetic capacity, and bioactive compounds, as well as their transcriptional level changes in Brassica rapa seedlings. Chlorophyll, carotenoid, and sugar content decreased, while proline and anthocyanins were significantly enhanced in the CuO NP-treated seedlings compared with the untreated controls. Reactive oxygen species (ROS), malondialdehyde (MDA), and hydrogen peroxide (H2O2) production were also enhanced in the seedlings exposed to CuO NPs, which could have caused DNA damage that was detected by a DNA laddering assay. The glucosinolate (GSL) and phenolic compound content were significantly increased in CuO NP-treated seedlings compared with that in control seedlings. Transcriptional variation of genes associated with oxidative stress (CAT, POD, and GST), R2R3-type MYB involved in GSL (BrMYB28, BrMYB29, BrMYB34, and BrMYB51), and phenolic compounds (ANS, PAP1, PAL, and FLS) biosynthesis was analyzed using real-time polymerase chain reaction. Significant upregulation of CAT, POD, GST, BrMYB28, BrMYB29, BrMYB34, BrMYB51, ANS, PAP1, PAL, and FLS genes was observed in seedlings exposed to different concentrations of CuO NPs relative to the untreated seedlings. Therefore, we suggest that the use of CuO NPs could stimulate the toxic effects and enhance phytochemicals (i.e., glucosinolates and phenolic compounds) in B. rapa.