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High protein intake can increase glomerular filtration rate (GFR) in response to excretory overload, which may exacerbate the progression of kidney disease. However, the direct association between glomerular hemodynamic response at the single-nephron level and dietary protein intake has not been fully elucidated in humans. In the present study, we evaluated nutritional indices associated with single-nephron GFR (SNGFR) calculated based on corrected creatinine clearance (SNGFR Cr ). We retrospectively identified 43 living kidney donors who underwent enhanced computed tomography and kidney biopsy at the time of donation at Jikei University Hospital in Tokyo from 2007 to 2018. Total nephron number was estimated with imaging-derived cortical volume and morphometry-derived glomerular density. SNGFR Cr was calculated by dividing the corrected creatinine clearance by the number of non-sclerosed glomeruli (Nglom NSG ). The mean (± standard deviation) Nglom NSG /kidney and SNGFR Cr were 685,000 ± 242,000 and 61.0 ± 23.9 nL/min, respectively. SNGFR Cr was directly associated with estimated protein intake/ideal body weight ( p = 0.005) but not with body mass index, mean arterial pressure, albumin, or sodium intake. These findings indicate that greater protein intake may increase SNGFR and lead to glomerular hyperfiltration.