Neisseria meningitidis group C is an encapsulated bacterium that causes several diseases and is associated with high mortality rates, thereby constituting a serious public health problem. Bio‐Manguinhos/Fiocruz is developing a conjugate vaccine by covalent attachment of capsular polysaccharide to hydrazide‐activated tetanus toxoid through reductive amination. It is necessary to quantify free components as a quality control process to prevent exacerbated adverse reactions and/or attenuation of vaccine immunogenicity. Thus, this study aimed to develop and validate a quality control method appropriate for the separation and quantification of free polysaccharide present in this conjugate N. meningitidis group C vaccine using CE. CZE was used to remove unbound polysaccharide, and the electrophoretic conditions were varied to optimize resolution. We were able to develop and validate the proposed method, which was linear and showed a matrix effect. Repeatability and partial reproducibility of the method were also evaluated. The robustness results showed that control of temperature is required for reliable results. The validated method will be used to evaluate the conjugate batches submitted for Phase III clinical studies and for routine quality control of the conjugate vaccine.