Alkaline phosphatase is a vital enzyme used in separation studies and as a biomarker for liver, bone, and certain cancer conditions. Its stability and specific properties enable insights into enzyme behavior, aiding in the development of detection methods with broader applications in various scientific fields. Alkaline phosphatase has four main isoenzymes: GCAP, IAP, PLAP, and TNAP, each with distinct roles. TNAP is found in the liver, kidney, and bones, playing a role in bone mineralization. The functions of the other isoenzymes are not fully known. Separation techniques like electrophoresis and chromatography are valuable for studying enzymes and proteins, revealing insights into their structure and function in pharmaceutical research and PTM studies. The main goal of this review paper is to thoroughly evaluate how capillary electrophoresis is applied to analyze alkaline phosphatase. It seeks to investigate the latest advancements in capillary electrophoresis and how they can improve the sensitivity, selectivity, and efficiency of alkaline phosphatase analysis.