Gel electrophoresis is a fundamental technique for the separation of charged molecules in pharmaceutical sciences, and it is widely employed in biochemistry, molecular biology, and genetics. The primary methods of electrophoresis include gel electrophoresis, zone electrophoresis, free-flow electrophoresis, and capillary electrophoresis, with gel and capillary electrophoresis being the most prevalent in biological research. In DNA electrophoresis, DNA fragments are separated based on the number of base pairs. This technique utilizes agarose gels, which facilitate the movement of DNA—characterized by a slight negative charge—toward the positive electrode at the gel's end. While the use of electrophoresis has diminished due to advancements in DNA sequencing and polymerase chain reaction (PCR) technologies, gel electrophoresis remains a valuable tool, especially for investigating the interactions of DNA with enzymes. Recent research indicates that scientists are employing agarose gel electrophoresis (AGE) to study enzyme inhibition, structure-activity relationships (SAR), binding studies, pharmaceutical formulation properties, DNA genomics and transcriptomics. Despite the prevalence of newer methodologies, gel electrophoresis continues to provide significant insights in the realm of DNA research. In this section, the recent studies of AGE will be indicated, and the role of AGE in the recent area of pharmaceutical research will be discussed to enlighten the future perspective.