Point-of-care testing (POCT) involves administering rapid on-site analysis to provide fast biochemical testing results. POCT reduces delays in clinical decision-making and eliminates the need to transport and prepare clinical samples for immediate diagnosis or clinical intervention by healthcare professionals. Herein, a novel methodology integrating thin-layer chromatography-based two-dimensional separation with miniature mass spectrometry was developed for rapid on-site clinical analysis. As a proof-of-concept demonstration, γ-aminobutyric acid, 2-hydroxyglutarate, and N-acetyl-l-aspartic acid, which are widely known as biomarkers for brain gliomas, were selected as model analytes for method development and validation. The proposed approach exhibited satisfactory analytical performance, with 1 ng/mL limits of detection, 2 ng/mL limits of quantitation, and recoveries in the range of 85.9-107.2%. Additionally, on-TLC derivatization and reactive spray ionization strategies were utilized to enhance the mass spectrometric signals compared to underivatized analysis. This method was applied to analyze clinical samples, showcasing its attractive potential outside the laboratory.