Cow milk allergy (CMA) is one of the most common food allergies worldwide, most frequently affecting infants and young children. Goat milk (GM) is widely advocated as a potential alternative source to cow milk due to its high digestibility, nutritional value, and hypo-allergenicity. Notwithstanding, protein homology between goat and bovine milk may still cause cross-reactivity and, hence may lead to allergic manifestations. Caseins are identified as one of the major milk allergens. In allergy management context, purified proteins are useful to precisely identify the specific milk protein the allergic individual is sensitive to. While enzymatic hydrolysis is commonly used to modify proteins to reduce their allergenicity, there is a lack of research on its efficiency with GM proteins. Therefore, the present work was undertaken to examine the effect of proteolysis using papain on the antigenicity of GM casein. Beforehand, Ion-exchange chromatography (IEC) was employed to study its effectiveness in extracting and purifying GM casein subunits. The one-factor-at-a-time (OFAC) approach was applied to optimize the process conditions to yield the highest degree of hydrolysis (DH). The antigenicity of the casein hydrolysate was evaluated based on the antibody binding capacity. The result showed that IEC was effective in purifying casein subunits of GM based on the distinctive bands observed on the SDS-PAGE of the collected fractions. The papain treatment (6 hours, 50 °C, pH 6.0, 1:20 enzyme: substrate (E:S) ratio) was determined to be the most optimum condition for GM casein hydrolysis (DH>50%) as assessed by the o-phthaldialdehyde (OPA) method, with E:S yielding the most significant difference (p<0.05). Both indirect and sandwich enzyme-linked immunosorbent assay (ELISA) approaches indicated that hydrolysis using papain can effectively reduce the allergenic potential of GM casein. The findings suggest papain-generated GM casein hydrolysate may be useful as an alternative protein source, particularly to produce innocuous foods for CMA patients.