CE is a promising technique for the analysis of glycosylated proteins, especially at the intact level. In the present study, the utility of CE for the separation of protein glycoforms is developed by using methyl chitosan as capillary coating. Methyl chitosan, in contrast to the polymers commonly used for coating, bears different types of amine groups, allowing for tunable charge states for various applications. The addition of methyl chitosan in background electrolyte can modulate the EOF and improve the separation performance. The methyl chitosan-coated capillary provided good separation of acidic or basic glycosylated proteins. Five ribonuclease B glycoforms were resolved by CE in less than 18 min, and the profile was essentially in agreement with that obtained by MALDI-TOF MS. The recombinant human erythropoietin glycoforms were well separated within 9 min. The developed method shows a great potential in protein glycoform analysis.