Hypothyroidism can occur due to deficiencies in micronutrients such as zinc, magnesium, and vitamin A. The aim of this study was to determine the effects of supplementation with these micronutrients on thyroid function, oxidative stress, and hs-CRP levels in patients with hypothyroidism. In a randomized double-blind, placebo-controlled trial with two parallel groups, 86 hypothyroid patients aged 20–65 were allocated to receive daily supplementation with either: (intervention group, n  = 43) one 30 mg zinc gluconate capsule per day, one 250 mg magnesium oxide tablet per day, and one 25,000 IU vitamin A capsule twice/week for 10 weeks or (placebo group, n  = 43) placebo capsules and tablets as above for 10 weeks. Neither of the groups changed their diet or physical activity. Thyroid hormones (free and total thyroxine (FT4 and TT4), free tri-iodothyronine (FT3), and thyroid-stimulating hormone (TSH)), oxidative markers (malondialdehyde (MDA) and total antioxidant capacity (TAC)), serum hs-CRP, and anthropometric indices (height and weight) were assessed at the baseline and at the end of the study. In the intervention group, we found a significant increase in serum FT4, decreased anthropometric indices, and lower levels of serum hs-CRP by the end of the 10 week protocol ( P  < 0.05). In the placebo group, serum TAC was decreased and hs-CRP increased ( P  < 0.05), with no significant changes in serum TSH, FT3, TT4, and MDA after the intervention. Zinc, vitamin A, and magnesium supplementation may have beneficial effects in patients with hypothyroidism and in diseases associated with hyperthyroidism.