Awareness of physical activity (PA) constraints in patients with primary hypothyroidism on thyroid hormone replacement therapy (THR) is important. Hence, this cross-sectional matched case-control study aimed to determine PA and sports participation (SP) in patients with hypothyroidism on THR in comparison to control subjects. Accordingly, survey questions were selected from the National Survey on Injuries and Physical Activity in the Netherlands (IPAN), supplemented with questions related to self-reported clinical characteristics and exercise-related constraints (ERC) of patients. In total, 1,724 female patients (mean age 53.0 years ±11.6) and 1,802 controls (mean age 52.6 ± 13.2) were included. Compared to controls, patients were less likely to comply with the moderate-intensity PA guideline (OR 0.70; 95% CI: 0.611-0.803), although patients were more actively participating in sports (OR 1.40; 95% CI: 1.156-1.706). Two-thirds of patients reported that hypothyroidism was limiting their PA performance. These limitations were more pronounced in patients with autoimmune thyroiditis (AIT) than in patients with hypothyroidism from other aetiology (OR 1.93; 95% CI: 1.518-2.457), representing disease-specific exercise intolerance. In order to establish effective intervention programmes to encourage regular PA in hypothyroid patients on THR with exercise intolerance, further research is warranted to better understand PA barriers.