(1) Background: PSMA ligand PET/CT is increasingly important for diagnostics of prostate cancer and other tumor diseases. In particular, the radiopharmaceutical [68Ga]Ga-PSMA-11 is widely used. Besides its tumor-specific binding, the uptake within the kidneys is dominant and seems to visualize the renal cortex specifically. Kidney diseases may alter the uptake of radiopharmaceuticals. Therefore, the correlation between renal uptake in PET/CT imaging and renal function should be investigated. (2) Methods: A group of 103 male patients were retrospectively evaluated for eGFR according to the CKD-EPI equation, tracer uptake intensity (SUVmax, SUVpeak, SUVmean), the molecular volume of the renal cortex, morphological kidney size, and total renal uptake. Manual and three different computer-assisted contouring methods (thresholds at 50% of SUVmax, 30% of SUVmax, and absolute SUV of 20) were used for measurements. Correlations between parameters were calculated using linear regression models. (3) Results: Renal SUVmax, SUVpeak, and SUVmean do not correlate with eGFR for manual or computer-assisted measurements. In contrast, molecular cortex volume shows a moderate correlation with eGFR (R2 = 0.231, p < 0.001), superior to morphological kidney size. A contouring threshold of 30% of SUVmax outperformed the other settings for renal cortex volume and total renal uptake. (4) Conclusions: Renal uptake of [68Ga]Ga-PSMA-11 cannot predict eGFR, but the functional renal cortex can be quantified by PET/CT imaging.