Interest in plant extracts as a natural source of antioxidants has grown significantly in recent years. The tree species Koelreuteria paniculata deserves attention due to its wide distribution, good adaptability, and growth to the degree of invasiveness in a number of European countries. The purpose of the present study was to analyze flavonoids and phenolic acids of the ethanol extracts from aerial parts of K. paniculata and to screen their antioxidant and DNA-protective activity. HPLC profiling revealed the presence of five flavonoids, with rutin (4.23 mg/g DW), hesperidin (2.97 mg/g DW), and quercetin (2.66 mg/g DW) as the major ones in the leaves, and (−)-epicatechin (2.69 mg/g DW) in the flower buds. Among the nine phenolic acids identified, rosmarinic, p-coumaric, salicylic, vanillic, and gallic acids were the best represented. All the extracts tested showed in vitro antioxidant activity that was determined by DPPH, ABTS, FRAP, and CUPRAC assays. The highest activity was recorded in the flower parts (in the range from 1133 to 4308 mmol TE/g DW). The DNA-protective capacity of the flower and stem bark extracts from the in vitro nicking assay performed, as well as the main diagnostic microscopic features of the plant substances, are given for the first time. According to the results obtained, the aerial parts of K. paniculata could be valuable sources of natural antioxidants.