Objectives: There is a paucity of data on impact of therapy of Hashimoto’s thyroiditis (HT) on catch-up growth. The objective of the study was to determine whether delayed diagnosis of HT and overt primary hypothyroidism has an impact on the catch-up of children and adolescents. Material and Methods: We conducted a prospective observational study over 3 years, in the thyroid clinic of a referral unit in South India. We assessed chronological age (CA), auxological parameters, clinical presentation, bone age (BA), and predicted adult height (PAH) in subjects with Hashimoto’s thyroiditis and overt primary hypothyroidism. Management and follow-up done as per standard protocols and study parameters reassessed after 1 year of therapy. Results: We recruited 38 subjects and divided them into two groups – Group 1 with BA within 2 standard deviations (SD) of CA (n = 20) and Group 2 beyond 2 SD (n = 18). During 1 year follow-up, height Z-scores were −0.1 ± 1.4 (baseline) and −0.1 ± 1.1 (endpoint) and −1.7 ± 1.7 (baseline) and −1.3 ± 1.3 (endpoint) in Groups 1 and 2, respectively. BA: CA ratio changed from 1.0 ± 0.1 to 1.0 ± 0.1 in Group 1 (P > 0.05) versus 0.7 ± 0.2 to 0.9 ± 0.1 in Group 2 (P < 0.05). The number of children who were pre-pubertal: pubertal changed from 15:5 to 11:9 in Group 1 and 14:4 to 7:11 in Group 2. For Group 1, baseline PAH Z score was −0.5 ± 1.7 and endpoint PAH Z score was −0.7 ± 1.6 versus a target height Z score of −1.1 ± 1.1 (P > 0.05); Group 2, the baseline PAH Z score −1.1 ± 1.6 and endpoint PAH Z score −2.2 ± 1.4 versus target height Z-score of −0.4 ± 1.7. Conclusion: Delayed diagnosis and treatment of juvenile autoimmune hypothyroidism results in permanent loss of height potential.