The herbicides diclofop-methyl and the fungicide difenoconazole are widely used in agriculture and may lead to serious toxicity risks. However, limited studies have been done to evaluate differences in the metabolic effects of these herbicides. Difenoconazole (10 mg/kg) and Diclofop-methyl (1 mg/kg) were orally administrated individually (Groups 1 and 2 respectively) as well as combined (G3) to rats for 28 days. In all treated groups, alanine aminotransferase (ALT) and urea were significantly higher than the control group. Plasma creatinine was also significantly higher in groups G1 and G2 than control. Significant inhibition in gamma glutamyltransferase (γGT) was observed in all treated groups, in addition to significant inhibition of plasma acetylcholinesterase enzyme (AChE) in G3 (p < 0.01). There was no effect in aspartate aminotransferase (AST) and albumin. Total plasma triiodothy- ronine (T3) hormone was significantly higher in groups G2 and G3 (p < 0.01), but significantly lower in G1 group as compared to control. Thyroxin (T4) was significantly lower in all treated groups than control. Cholesterol level was significantly lower in G3 than control, and a total protein (TP) was significantly higher in all treated groups than control. No differences were observed in glucose levels. Malondialdehyde (MDA) and superoxide dismutase (SOD), an oxidative stress biomarker, was significantly increased in all treated groups comparing to control. Sulphur containing protein (SH-protein) was significantly lower in G1 than control. No significant changes were observed for GST in all treatments. The significant differences in measured biomarkers after application of diclofop-methyl, difenoconazole individually and combined indicate that the investigated pesticides may have potentially harmful effects on humans and the surrounding environment. We suggest that larger studies be conducted to better understand the toxicity mechanisms of these pesticides.