Background: Primary hypothyroidism (PH) is a common chronic life style disorder. Whole system Ayurveda protocol on PH (WSAPH) is explored for it's possible complimentary role in the management of suboptimal controlled PH on stable levothyroxine therapy. Objective: To evaluate the efficacy of whole system Ayurveda protocol on Primary hypothyroidism with suboptimal response to stable levothyroxine therapy. Material and methods: Study was a randomized controlled trial. Total 46 known patients of suboptimal response to stable levothyroxine therapy, age group 20-60 years of either sex participated in the study. They were randomly placed in two groups, Group KG received Kanchanara guggulu two tablets of 500 mg each, thrice a day with water and group WSAPH was on whole system Ayurveda protocol for primary hypothyroidism (WSAPH). Interventions were for 60 days. Assessments were done through various parameters like Thyroid profiles (TSH, T3, T4, Free T4), Weight, BMI, Skin fold thickness (SFT), Body fat index (BFI), Waist hip ratio (WHR), Lipid profile, Zulewskis clinical score for hypothyroidism (ZUL), WHO Quality of Life- BREF (WHOQOL-BREF), Clinical Global Improvement scales (CGI). Clinical assessments were done on every 15th day and biochemical were done before and after interventions. Results: Study showed that WSAPH group produced significant outcome improvement compared to KG group in TSH (p = 0.02), weight (p = 0.02), SFT (p = 0.04), BFI (p = 0.01), WHOQOL-BREF (p = 0.004) and ZUL (p = 0.02). Both the group showed improvements in BMI, WHR, BFI, SFT, WHOQOL-BREF, ZUL, CGI scales. Effect size was medium in TSH, weight, BFI, SFT and ZUL. Conclusion: WSAPH was effective in management of PH and normalized TSH and ZUL scores in patients with suboptimal response to stable levothyroxine therapy. Further studies are needed.