Background Hypothyroidism (HT) is the most prevalent endocrine disorder, affecting approximately one in 10 out of 35 adults, with a higher prevalence in females and the elderly. Purpose This systematic review (SR) aimed to discuss the effects of yoga on markers and comorbid conditions of HT. Methods The SR was registered with the PROSPERO (PROSPERO 2022 CRD42022312990). Google Scholar, PubMed, Cochrane, and EMBASE were searched for the relevant English language interventional studies published from 31 December 1947 to 31 December 2023 by using the keywords ‘meditation OR breath regulation OR yoga OR yoga nidra AND hypothyroidism OR hypothyreosis OR underactive thyroid OR low thyroid’. Of the 4078 screened studies, eight eligible studies (three RCTs, two pilot studies, two pre-post trials, and one case study) with 421 HT patients (392 females and 29 males) and three to six-month yoga interventions were included. Two independent review authors extracted study characteristics and synthesised them descriptively. RCTs and NRSIs were assessed for risk-of-bias (RoB) using Cochrane tools RoB2 and ROBINS-1. Results The findings suggest that yoga effectively improves the thyroid profile, lipid profile, heart rate variability, pulmonary functions, anxiety, depression, and quality of life among HT patients. Conclusion Yoga may be an inexpensive add-on preventive and therapeutic option for HT. The clinical and methodological heterogeneity among the studies did not allow for meta-analysis (MA). Well-designed MAs are warranted by including rigorous RCTs to draw valid conclusions and defined mechanisms regarding the efficacy of yoga practices/interventions on HT.