Background and objective Chronic kidney disease (CKD) is a clinical syndrome characterized by the irreversible loss of kidney function. It is a widespread condition affecting populations worldwide. The kidneys play a crucial role in the metabolism, breakdown, and elimination of thyroid hormone and thyroid-stimulating hormone (TSH). Consequently, thyroid dysfunction can occur as an endocrine manifestation in CKD patients. Previous studies investigating thyroid abnormalities and the severity of CKD have yielded diverse outcomes. In light of this, this study aimed to determine the prevalence of thyroid dysfunction in CKD patients and explore the association between different thyroid dysfunctions and markers of kidney function. Methods A total of 140 CKD patients who met the inclusion criteria were recruited, and their demographic details and routine investigations were recorded. Blood samples were collected for kidney function tests and thyroid function tests. The primary outcome measures included markers of kidney function [urea, creatinine, and estimated glomerular filtration rate (e-GFR)] and thyroid profile [TSH, free thyroxine (FT4), and free triiodothyronine (FT3)]. Mean and standard deviation (SD) were calculated for continuous variables, while frequencies were calculated for categorical data. Fisher's exact test was employed to evaluate the association between two categorical variables, and p-values below 0.05 were considered statistically significant. Results The mean (± SD) urea, creatinine, and e-GFR were found to be 139 (± 81.1) mg/dL, 5.33 (± 4.1) mg/dL, and 20.1 (± 15) ml/min/1.73 m2, respectively. Of note,133 (95%) patients had elevated urea levels, with the majority (n = 109, 77.8%) having urea levels between 40 and 199 mg/dL; 70 (50%) patients had creatinine levels less than 4 mg/dL, and 107 (76.4%) had e-GFR of less than 30 ml/min/1.73 m2. The mean (± SD) TSH, FT4, and FT3 levels were found to be 6.64 (± 11.2) mIU/ml, 13.6 (± 4.54) pmol/L, and 2.65 (± 1.89) pmol/L, respectively. It was observed that 18 (12.9%, 95% CI: 8.29-19.4%) of the CKD patients had hypothyroidism and 21 (15%, 95% CI: 10.02-21.8%) had subclinical hypothyroidism (SCH), while only two (1.4%, 95% CI: 0.39-5.05%) and five (3.6%, 95% CI: 1.5-8.08%) had hyperthyroidism and subclinical hyperthyroidism, respectively. Thirty-nine (27.9%, 95% CI: 21.1-35.8%) patients had low FT4 levels, whereas a considerable majority (n = 123, 87.9%, 95% CI: 81.41-92.28%) of the patients suffering from CKD were found to have low FT3 levels. The associations of urea levels with SCH, low FT4, and FT3 status were found to be statistically significant with p-values of 0.002, 0.033, and <0.001, respectively. The association between e-GFR and low FT3 status was also statistically significant, with a p-value of 0.014. Conclusion Nine out of 10 patients with CKD were discovered to have low FT3 levels, whereas one in four patients had low FT4 levels. The study participants also exhibited a significant presence of SCH and hypothyroidism, with prevalence rates of 15% and 12.9%, respectively. Urea levels and e-GFR, indicating the severity of CKD, showed a significant association with the presence of various thyroid abnormalities. Hypothyroidism in CKD patients can complicate disease progression, impact mortality rates, and affect overall quality of life. Therefore, routine screening for thyroid abnormalities should be conducted in all CKD patients.