Our previous study revealed that thyroid cysts might have a beneficial effect on thyroid hormone activation. Subclinical hypothyroidism is reportedly associated with chronic kidney disease (CKD). Since systolic hypertension is associated with hyperthyroidism and thyroid cysts are associated with systolic hypertension, the presence of thyroid cysts could be inversely associated with CKD, especially in patients with systolic hypertension. Such an association could indicate that thyroid cysts have a beneficial effect on thyroid hormone activation. To investigate systolic hypertension status-specific associations between thyroid cysts and CKD, a cross-sectional study with 1,750 individuals aged 40–74 years who participated in annual health check-ups was conducted. Independent of thyroid hormone levels (free triiodothyronine (T3) and thyroid-stimulating hormone (TSH)), the presence of thyroid cysts was significantly inversely associated with CKD in subjects with systolic hypertension, but not in subjects without systolic hypertension. The adjusted odd ratios and 95% confidence intervals were 0.52 (0.28, 0.98) for subjects with systolic hypertension and 1.11 (0.82, 1.50) for subjects without systolic hypertension. Thyroid cysts might affect CKD in a beneficial manner. Systolic hypertension could act as an effect modifier on the association between thyroid cysts and CKD. These findings could help clarify thyroid-related mechanisms of CKD development.