No current studies are available on application and side effects of potassium iodide iontophoresis. This study assessed the potassium iodide iontophoresis effect in the throat and larynx area on TSH, FT3 and FT4 hormone levels. Double-blinded randomized controlled trial with 1:1 parallel-group was conducted at the University of Rzeszow, Poland. A total of 50 healthy volunteers with normal TSH, FT3, FT4 levels without focal changes in the thyroid ultrasonography were subjected to 10 electrotherapy treatments (galvanization and iontophoresis groups). TSH, FT3, FT4 levels were determined before 10 treatments (test 1), 2 weeks after their completion (test 2) and after 6 months (test 3). In tests 2 and 3, both groups had normal levels of TSH, FT3, and FT4. No statistically significant differences between the galvanization and iontophoresis groups were found in terms of change of TSH, FT3, FT4 levels between tests 1 vs. 2 and 1 vs. 3. Both groups had lower levels of all measured parameters in test 3. Potassium iodide iontophoresis does not affect thyroid hormone levels in the short and long term. It is advisable to continue the follow-up study with larger groups to confirm the safety of electrotherapy procedures in the pharynx and larynx area.