Affinity capillary electrophoresis (ACE) has been widely applied to evaluate binding constants of various systems. Recently, moment equations were derived based on the moment analysis (MA) theory for describing the influence of reaction kinetics and longitudinal diffusion on the elution peak profiles measured by ACE (MA-ACE). The equations enable one to obtain not only the binding constants but also the reaction rate constants from the migration time and variance of elution peaks. However, it is necessary to consider other factors (e.g., sample injection, detector window, Joule heating, and ramp time of the voltage increase) to improve the accuracy of MA-ACE. The variance of these effects was quantified under typical experimental conditions. Such quantification clarified the process to obtain the rate constants. The best experimental conditions to achieve high accuracy were discussed.