Peroxynitrite anion (ONOO-) is an important in vivo oxidative stress biomarker whose aberrant levels have pathophysiological implications. In this study, an electrochemical sensor for ONOO- detection was developed based on graphene nanoplatelets-cerium oxide nanocomposite (GNP-CeO2) incorporated polyaniline (PANI) conducting hydrogels. The nanocomposite-hydrogel platform exhibited distinct synergistic advantages in terms of large electroactive surface coverage and providing a conductive pathway for electron transfer. Besides, the 3D porous structure of hydrogel integrated the GNP-CeO2 nanocomposite to provide hybrid materials for the evolution of catalytic activity towards electrochemical oxidation of ONOO-. Various microscopic and spectroscopic characterization techniques endorsed the successful formation of GNP-CeO2-PANI hydrogel. Cyclic voltammetry (CV) measurements of GNP-CeO2-PANI hydrogel modified screen-printed electrodes (SPE) were carried out to record the current changes influenced by ONOO-. The prepared sensor demonstrated a significant dose-dependent increase in CV peak current within a linear range of 5-100 µM (at a potential of 1.12 V), and a detection limit of 0.14 with a sensitivity of 29.35 ± 1.4 μA μM-1. Further, a customized microfluidic flow system was integrated with the GNP-CeO2-PANI hydrogel modified SPE to enable continuous electrochemical detection of ONOO- at low sample volumes. The developed microfluidic electrochemical device demonstrated an excellent sensitivity towards ONOO- under optimal experimental conditions. Overall, the fabricated microfluidic device with hybrid hydrogels as electrochemical interfaces provides a reliable assessment of ONOO- levels. This work offers considerable potential for understanding the oxidative stress-related disease mechanisms through determination of ONOO- in biological samples.