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Background Primary palmar hyperhidrosis causes a lot of problems for patients and negatively affects their quality of life. Currently, iontophoresis with tap water and aluminum chloride hexahydrate is used for primary palmar hyperhidrosis. Yet, little evidence exists about iontophoresis with aluminum chloride hexahydrate in the form of gel. This study investigated the effect of aluminum chloride hexahydrate gel iontophoresis compared to tap water iontophoresis on primary palmar hyperhidrosis. Methods In this randomized controlled trial study, 32 patients with primary palmar hyperhidrosis were divided randomly into two groups (n = 16). Participants received 7 sessions of iontophoresis with aluminum chloride hexahydrate gel or tap water every other day on the dominant hand. The sweating rate was measured by gravimetry and iodine–starch tests before and after the last treatment session. Results Following the iontophoresis, the rate of sweating in both hands in the two groups was significantly reduced (P < 0.001). However, the sweating rate in the treated hand and the non-treated hand showed no significant difference. There was no significant difference observed in sweating rate reduction between both groups over time, but the larger effect size values observed in the aluminum chloride hexahydrate gel iontophoresis group may suggest the superiority of this gel over tap water in reducing the rate of sweating. Limitation Further investigations with longer follow-up are needed to confirm the hypothesis regarding the effectiveness of aluminum chloride hexahydrate gel iontophoresis over other types of iontophoresis. In addition, contraindications of iontophoresis such as pregnancy, pacemakers, and epilepsy should be considered. Conclusion The present study provides preliminary evidence suggesting that aluminum chloride hexahydrate gel iontophoresis is an effective alternative treatment to decrease sweating rate in extended areas with fewer side effects in patients with primary palmar hyperhidrosis.