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Background: Hypothyroidism is among the most prevalent endocrine disorders globally, affecting millions of adults—particularly women. Although levothyroxine remains the standard of care, a significant subset of patients continues to experience symptoms despite biochemical normalisation. Individualised homoeopathic therapy, which addresses the constitutional totality of the patient, represents a complementary approach warranting clinical evaluation. Methods: A randomised controlled trial was conducted at the institutional and peripheral OPDs of Dhanwantari Homoeopathic Medical College, Nashik. Thirty adult patients (25–65 years) with confirmed hypothyroidism were enrolled and randomly assigned to two groups of 15 each: Group A (individualised homoeopathic medicines) and Group B (standardised allopathic therapy). Outcome was assessed by change in serum TSH levels and overall symptomatic improvement. Results: Of 30 patients, 23 (76.7%) showed significant improvement. Group A (homoeopathic) recorded an 86.7% improvement rate (13/15) versus 66.7% (10/15) in Group B. Post-treatment, patients with TSH < 5 mIU/L increased from 30.0% to 40.0%. Natrum Muriaticum, Pulsatilla and Phosphorus were the most frequently prescribed homoeopathic remedies. Conclusion: Individualised homoeopathic medicines demonstrated a clinically meaningful advantage over standardised allopathic therapy in symptom relief and TSH normalisation, supporting their role as effective add-on therapy.