In recent years, there have been efforts to develop therapeutic agents that target metabolic enzyme systems in addition to existing treatment in possible cancer treatments. Cyclophosphamide (CYP) is an anticancer drug commonly used in various cancer treatments. Chrysin (CH) and naringin (NR) are natural flavonoids that possess many medicinal and pharmacological properties. In the present study, we aimed to investigate the effect of CH and NR against CYP-induced toxicity on some metabolic enzyme activities. For this purpose, 56 male rats were randomly divided into 8 groups in our in vivo study. The rats were pretreated with CH (25 and 50 mg/kg bw) and NR (50 and 100 mg/kg bw) for 7 days before administering a single dose of CYP (200 mg/kg bw) on the seventh day. According to the in vivo results of our study, it was observed that CH and NR regulated abnormal changes in CYP-induced enzyme activities. In addition, our in vitro study, G6PD enzyme was purified from rat erythrocyte using affinity chromatography. The effects of CH, NR, and CYP were investigated on the purified enzyme. It was determined that CH increased the enzyme activity, CYP ineffective on the enzyme activity, whereas NR inhibited the enzyme activity noncompetitively. Graphical abstract.