Gastrodia elata, a traditional Chinese medicinal herb, undergoes processing with ginger to enhance its therapeutic properties. This study investigated the impact of ginger processing on the quality control of G. elata using electrochemical fingerprint technology and high-performance liquid chromatography (HPLC). The electrochemical fingerprint conditions were optimized, and the fingerprints of raw and ginger-processed G. elata samples were compared. The HPLC analysis revealed significant changes in the contents of gastrodin, parishin A, and parishin B after processing. The electrochemical fingerprints exhibited distinct differences between raw and ginger-processed samples, with improved batch-to-batch consistency in the latter. Principal component analysis and hierarchical cluster analysis demonstrated the correlation between the electrochemical fingerprints and HPLC results. The findings highlight the potential of electrochemical fingerprint technology as a complementary tool to HPLC for the comprehensive quality assessment of G. elata. This study provides valuable insights into establishing standardized processing protocols and quality control strategies for G. elata, emphasizing the importance of combining multiple analytical techniques for ensuring the consistency, safety, and efficacy of herbal medicines.