Background: Iron deficiency is the most common micronutrient deficiency affecting nearly one-third of the population and is the leading cause of anemia worldwide. n this study, we evaluated the effectiveness of ferrous gluconate and ferrous sulfate supplements to identify the best iron supplement with the most effective and the least side effects in toddlers 6-24 months old. Methods: A randomized, single-blind clinical trial was performed. A total of 120 healthy toddlers aged 6 to 24 months old (two groups of 60) entered the study. Toddlers receiving ferrous sulfate (FS group) and ferrous gluconate (FG group) supplements. Blood indices such as hemoglobin & ferritin levels were evaluated at baseline and 6 months post- supplementation. Results: The FG group that received ferrous gluconate chelate iron showed approximately 2.4 g/dl higher Hb level in comparison to the FS group with ferrous sulfate supplementation 6 months post-supplementation (12.51±0.58 g/dL vs. 10.10±0.83, p = 0.045). Side effects were significantly more common in the FS group than the FG group (43.3 % vs. 16.7 %, P ≤ 0.001. Conclusion: The present study shows that educating mothers to feed toddlers with breast milk and iron supplements, including ferrous sulfate and ferrous gluconate, can be helpful in the prophylaxis of iron deficiency. Our results show that ferrous gluconate can be used in cases where ferrous sulfate causes unacceptable side effects.