Electrophoresis is a practical diagnostic tool for the identification of changes in serum protein fractions, which can be associated with a variety of diseases. Protein electrophoresis studies in Ursidae are limited, and currently no published fraction values are available for the giant panda (Ailuropoda melanoleuca). The aim of this study was to describe the serum protein fractions in the giant panda using both capillary zone electrophoresis (CZE) and standard agarose gel electrophoresis (AGE) techniques. Serum samples from nine healthy giant pandas (n = 19) were used for this study. Samples were evaluated using CZE and standard AGE. The CZE procedure successfully resolved serum proteins into seven fractions: prealbumin; albumin; and α1-, α2-, β1-, β2-, and γ-globulin; while AGE separated serum into only six protein fractions: prealbumin; albumin; α1-, α2-, and β-globulins; and γ-globulin. These data will serve as a preliminary baseline for further studies and provide insight for the medical management of giant pandas.