Background/Objectives <p>The interplay of subclinical hypothyroidism (SH) with obesity has been well-documented, while an intriguing but still controversial association with kidney damage (KD) has recently emerged. Given the heightened cardiometabolic risk inherent to pediatric obesity, this might further impact on the overall health of children with obesity. Therefore, we aimed at evaluating the impact of SH on KD in children with obesity.</p> Subjects/Methods <p>We retrospectively examined 355 children with obesity stratified according to presence or absence of SH. KD was defined as reduced estimated glomerular filtration rate (eGFR&lt;90 mL/min/1.73 m²) and/or hypertension, and/or albuminuria (≥30 mg/g urinary creatinine), while SH was defined by thyroid stimulating hormone (TSH) &gt; 4.5μ UI/ml with normal free triiodothyronine and free thyroxine levels.</p> Results <p>Children with SH showed a higher KD prevalence than those without SH (<i>p</i> = 0.004). They also had lower eGFR levels than their counterparts without SH (<i>p</i> = 0.001) and showed an adjusted OR to have KD of 2.04 (95% CI: 1.15–3.61; <i>p</i> = 0.015). A general linear model for eGFR variance showed an inverse association of eGFR with TSH levels (<i>p</i> &lt; 0.0001).</p> Conclusions <p>Although preliminary, our data suggested an increased risk of KD in children with obesity and SH.</p>