Abstract Background Thyroid hormones play a key role in testicular development, particularly in the regulation of Sertoli cell proliferation and differentiation. While congenital hypothyroidism is common and treatable, the effects of thyroid hormone insufficiency on early testicular development during the neonatal period remain unclear. Objectives This study investigated the effects of transient and continuous hypothyroidism during the neonatal and prepubertal periods on testicular development, focusing on spermatogonial stem cell dynamics through histological and germ cell marker analyses. Materials and methods We established two neonatal rat models using 6‐n‐propyl‐2‐thiouracil: a continuous hypothyroidism model and a transient neonatal hypothyroidism model. 6‐n‐Propyl‐2‐thiouracil was administered to lactating dams at concentrations of 0.001%, 0.01%, and 0.03%. Male offspring were evaluated on postnatal days 7, 10, and 20 for serum hormone levels, body and testicular growth, and immunohistochemical markers (GFRA1, DDX4, SOX9, and Ki‐67). Results The transient hypothyroidism model successfully induced transient hypothyroidism without systemic growth impairment. Serum thyroxine and thyroid‐stimulating hormone levels were normalized by day 20. GFRA1‐positive undifferentiated germ cells consistently increased in all 6‐n‐propyl‐2‐thiouracil groups on days 7 and 20. Co‐expression with Ki‐67 indicated cell proliferation. The formation of seminiferous tubule lumen was reduced in a dose‐dependent manner. Discussion Transient neonatal hypothyroidism increases the number of undifferentiated germ cells, potentially including spermatogonial stem cells. The transient hypothyroidism model minimizes systemic effects and allows the observation of testis‐specific responses to thyroid disruption. Conclusion This study demonstrated that even low‐dose transient hypothyroidism during the neonatal period enhances the population of undifferentiated germ cells, potentially including spermatogonial stem cells. The transient hypothyroidism model offers a physiologically relevant and minimally invasive platform to explore how early thyroid hormone imbalances influence germ cell population establishment during a critical window of testicular development, potentially reflecting the clinical scenarios of treated congenital hypothyroidism.