The present study was conducted to examine cytokine profiles in the masseter muscle before and after complete Freund's adjuvant (CFA)-induced inflammation and possible sex differences in the cytokine levels. Age matched male and female Sprague Dawley rats were injected with CFA in the mid-region of the masseter muscle. Muscle tissue surrounding the injection site was extracted 6 h, 1, 3 and 7 days after the injection to measure TNF-α, IL-1β, IL-6 and IL-4 levels with Luminex multi-analyte profiling (xMAP) technology. The cytokine levels were compared to those obtained from naïve rats. CFA injection into the masseter muscle led to a significant time effect in the level of TNF-α compared to that of naïve rats. The pattern of changes in TNF-α level after CFA injection was significantly different between the male and female rats owing to the differences in basal levels. CFA injection induced significant time-dependent increases in the levels of IL-1β and IL-6 in the masseter muscle in both male and female rats. The level of IL-4 was slightly, but significantly, reduced in both sexes at 6 h and 3 days after CFA-induced inflammation. No significant sex differences were observed in the levels of IL-1β, IL-6 or IL-4. The results provided novel information about distinct cytokine profiles during CFA-induced muscle inflammation, and the basis for further pursuing contributions of each cytokine in pain processing and analgesic responses in both sexes.