One of the critical factors governing the application of membrane technology for the commercial production of PEGylated proteins is membrane fouling. The objective of this study was to examine the effects of PEGylation on the filtrate flux and fouling characteristics during ultrafiltration of a model PEGylated protein using both fully and partially retentive regenerated cellulose and polyethersulfone membranes. The physical characteristics of the native and PEGylated proteins were evaluated by size exclusion chromatography, dynamic light scattering, capillary electrophoresis, and reverse-phase chromatography. The filtration behavior with the cellulose membranes was dominated by concentration polarization effects, with the lower flux for the PEGylated proteins associated with the smaller bulk mass transfer coefficient. Significant fouling was observed with the polyethersulfone membranes. Greater fouling was seen with the PEGylated protein due to its increased size, greater hydrophobicity, and lower electrostatic interactions, all of which are directly associated with the attached poly(ethylene glycol) chains. These results provide important insights into the ultrafiltration characteristics of PEGylated proteins.