Background: Emerging evidence shows a bi-directional talk between the kidney and thyroid; yet to date, sparse data exist as to the screening and treatment of hypothyroid states, whether Subclinical Hypothyroidism (SCH) or Clinical Hypothyroidism (CHT), in Chronic Kidney Disease (CKD) patients. Objectives: The aim of the current study was to examine the association between thyroid hypofunction (whether subclinical or clinical) and proteinuric CKD (low eGFR and/or proteinuria), and to assess the impact of treating thyroid hypofunction on the progression of CKD. Patients and methods: We conducted a prospective cohort study on 100 participants with baseline proteinuric CKD who were subcategorized according to their thyroid status into three groups: 20 euthyroid, 40 (SCH), 40 (CHT). All subjects were then followed up for 2 years after receiving Thyroid Hormone Replacement Therapy (THRT) according to their thyroid status. Results: At baseline, we found a highly statistically significant association between SCH/CHT and low eGFR and proteinuria (P-value 0.001 for both) in univariate and multivariate analyses. After THRT, we found a statistically significant reduction in CKD progression as evidenced by preservation of mean eGFR and decrease in proteinuria in both groups with SCH and CHT (P-value 0.001 and 0.016 respectively) after the first 6 months of treatment that persisted over the remainder of 2-year follow-up period at a P-value 0.001. Conclusion: The current study demonstrated a strong association between baseline proteinuric CKD and hypothyroid states and showed that THRT significantly halted CKD progression in hypothyroid patients who achieved euthyroid state.