The objective of this study was to determine the effect of fluoride (F) and arsenic (As) on the activity of acetylcholinesterase (AChE), a critically important nervous system enzyme, and to test the protective role of buffalo epiphyseal (pineal) proteins (BEP) in rats. Arsenic (20 mg/kg BW, intraperitoneally) and F (150 ppm, perorally) were exposed, and BEP was administered intraperitoneally (100 μ g/kg BW) along with F and As to rats for 7 days. As and F exposure significantly (p < 0.05) increased their levels in plasma and decreased the activity of AChE in plasma, RBCs, heart, and brain of rats. Interestingly, As- and F-induced inhibition of AChE activities increased As and F levels in plasma, and organs were significantly (p < 0.05) counteracted by BEP administration. These findings indicate the protective role of buffalo (Bubalus bubalis) epiphyseal proteins on F- and As-induced adverse changes in AChE activity as a candidate biomarker for neurotoxicity in female rats.