Sphingomyelinase (SMEnzyme) converts sphingomyelin into ceramide, modulating membrane properties and signal transduction which inactivates mutations and causes Niemann–Pick disease. Real‐time monitoring of SMEnzyme is also crucial as an important biomarker for several other diseases like atherosclerosis, multiple sclerosis, and HIV. In this study, we present an electrochemical method to detect SMEnzyme concentration that is more sensitive and much faster than currently available commercial assays. For detection and the amplification of the SMEnzyme signal, methylene blue (MB)-encapsulated sphingomyelin (SM)-based liposome with 50% cholesterol was synthesized via sonication method. Then the target SMEnzyme causes the free release of the MB from the MB-liposome formulation which can be detected on GCE||Au-PAni/N,S-GQDs electrode, prepared via interfacial polymerization and then self-assembly approach. The change of SM to gel state bilayer with increasing concentration of ceramide accounts for the observed increase in membrane permeability and consequent release of encapsulated MB as the redox indicator for electrochemical Differential Pulse Voltammetric (DPV) analysis. To get the optimum capture through π–π stacking interaction of the released MB on the Au-PAni/N,S-GQDs nanocomposites, which has been used as working electrode. Minimal cross-reactivity with similar phospholipase and proteins confirms the stable and non-leaky MB-liposome platform with low background signal and high specificity toward SMEnzyme. Additionally, the applicability of the proposed sensor has successfully verified in three possible sources of human serum, plasma and cell supernatant without compromising its performance. Taken together, the simplicity, rapid response time and high sensitivity of this present method offer huge potential in point-of-care diagnostics of SMEnzyme detection.