Objectives: The incidence and prevalence of chronic kidney disease (CKD) are rising worldwide. It is becoming more common in the developing world with the increasing impact of non-communicable diseases in these countries. Also, autoimmune disorders, including thyroid dysfunction are more common and may worsen the clinical status of patients with CKD. We sought to determine the thyroid status in patients with CKD and explore the clinical, biochemical, immunological, and hematological parameters that can be affected by thyroid dysfunction among CKD patients. Methods: We conducted a cross-sectional observational study at the Royal Hospital, Muscat. The data was progressively collected for all newly diagnosed CKD patients with no known history of thyroid disease from January 2018 to December 2019. Assessment of thyroid status was performed at their initial diagnosis. Results: During the study period, 121 females (40.3%) and 179 males (59.7%) were diagnosed with CKD with no prior thyroid diseases. The mean age for females and males were 53.6±16.5 and 49.5±16.5 years, respectively. There were 35 patients with thyroid dysfunction with a prevalence of 11.7%. Of these, 22 patients (62.9%) had subclinical hypothyroidism, and 13 (37.1%) had subclinical hyperthyroidism. Total cholesterol and low-density lipoprotein were higher in hypothyroid patients. Urea was higher in hyperthyroid patients with CKD, and hemoglobin level was significantly lower. Conclusions: Thyroid dysfunction was not uncommon among CKD patients, with subclinical hypothyroidism more common than subclinical hyperthyroidism. Thyroid dysfunctions coexisted with kidney dysfunction. These hormonal axis dysfunctions may not be apparent at first presentation; and therefore, may require close clinical and laboratory evaluations.