Introduction: Thyroid dysfunction is a prevalent endocrine disorder in patients with chronic kidney disease (CKD). This study aimed to evaluate the status of thyroid hormone profile in different stages of CKD and explore the associations between thyroid dysfunction and clinical variables. Methods: A cross-sectional study was conducted among 100 CKD patients admitted at Tertiary care centre. Demographic and clinical data, along with thyroid hormone levels, were collected and analyzed. Statistical analysis was performed using descriptive statistics, chi-square test, and odds ratios. Results: The prevalence of thyroid dysfunction among CKD patients was 39%, with subclinical hypothyroidism being the most common type (22%), followed by overt hypothyroidism (10%). No significant differences were observed in age or sex distribution among different CKD stages (p > 0.05). There were no significant associations between thyroid dysfunction and the presence of diabetes mellitus, hypertension, or cardiovascular disease in CKD patients (p > 0.05). The levels of urea, creatinine, and estimated glomerular filtration rate varied significantly across CKD stages (p < 0.01). However, thyroid hormone levels (Free T3, Free T4) did not show significant differences among stages, except for thyroid-stimulating hormone (TSH) (p < 0.01). Conclusion: This study highlights the high prevalence of thyroid dysfunction in CKD patients, predominantly characterized by subclinical hypothyroidism. Age, sex, diabetes mellitus, hypertension, and cardiovascular disease showed no significant associations with thyroid dysfunction. The levels of urea, creatinine, and eGFR varied significantly across different CKD stages, indicating the impact of kidney function on thyroid hormone regulation. Further research is needed to better understand the complex relationships between thyroid dysfunction, comorbidities, and CKD.