Pesticides are suspected of being endocrine disruptors. This cross-sectional study measured serum samples for levels of thyroid hormones including thyroid stimulating hormone (TSH), triiodothyronine (T3), thyroxine (T4), free T3 (FT3), and free T4 (FT4) among Indonesian female farmers (n = 127) and non-farmers (n = 127). A questionnaire was used to collect information on demographics and risk factors including work characteristics and frequency, and the use of home and agricultural pesticides. Results showed that there were no significant differences in the distribution of the clinical categories of thyroid levels between farmers and non-farmers except for FT3 and T4. However, in multivariable regression controlling for confounders, FT3 and T4 were significantly higher for farmers compared to non-farmers. In addition, 32% of farmers had clinically low iodine levels and 49% of non-farmers had clinically high iodine levels. We conclude that pesticide exposure may not be as important as iodine intake in explaining these findings. We recommend counseling by health workers about the importance of using iodized salt for farmers and counseling about high iodine foods that need to be avoided for non-farmers.