Protein sieving, which is a fundamental tool in the biotechnology field, can be automated using capillary gel electrophoresis. The high-viscosity and biocompatible linear gels required for capillary sieving must be replaced for each run using high pressures. Thermally responsive gels are easier to renew in the capillary as they can be repetitively switched between low- and high-viscosity solutions. A thermally responsive sieving gel was recently demonstrated to separate DNA, which is a larger biomolecule than proteins. This material required no synthesis as it was self-assembled from common phospholipids. Nanogels composed of dimyristoyl-sn-glycero-2-phosphocholine and 1,2-dihexanoyl-sn-glycero-3-phosphocholine exhibit thermally reversible viscosity within a 10 °C temperature change, forming a sieving matrix above 24 °C. Additionally, these nanogels are nondenaturing and have been demonstrated to preserve the activity of enzymes. In this report, a phospholipid nanogel is used for the first time for capillary gel electrophoresis separations of proteins. The mobilities in buffer and nanogel demonstrated that 20-30% nanogel supports sieving of proteins ranging from 20 to 80 kDa. Capillary separations based on sieving rather than electrophoresis had similar precision in both area and migration time as well as similar separation efficiencies. However, the migration time increased with gel concentration. The nanogel was used for the analysis of proteins in human serum. Proteins in the sample were more effectively resolved and quantified with capillary sieving compared to free-solution capillary electrophoresis. This allowed for accurate quantification.