We report a 15-year-old boy from Karnataka, India, initially misdiagnosed as HbE/β-thalassemia. On follow-up, Capillary electrophoresis (CE) showed a 3.3% peak in Zone 4, with the WBC Differential Fluorescence (WDF) scattergram on the Sysmex XN 10 instrument suggesting an unstable hemoglobin. CE pattern, along with heat stability testing, mass spectrometry, and molecular sequencing, confirmed Hb Köln (β98 Val → Met), also detected in his father. This case emphasizes the need to suspect unstable hemoglobins in unexplained hemolysis and highlights the diagnostic value of CE and WDF scattergram.