This work presents the detection of hypoxanthine (HXA), a purine derivative that is similar to nucleic acids who overconsumption can cause health issues, by using hydrothermally synthesized cerium phosphate (CePO4) followed by a sonochemical approach for CePO4 decorated with a functionalized carbon nanofiber (CePO4@f-CNF) nanocomposite. The formation of the nanocomposite was confirmed with X-ray powder diffraction (XRD), scanning electron microscopy (SEM), and energy-dispersive spectroscopy (EDS). A CePO4@f-CNF nanocomposite is used to modify a glassy carbon electrode (GCE) to analyze the electrochemical detection of HXA. Cyclic voltammetry (CV), Electrochemical impedance spectroscopy (EIS), and Differential pulse voltammetry (DPV) were used to examine the electrochemical properties of the composite. As a result, the modified electrode exhibits a larger active surface area (A = 1.39 cm2), a low limit of detection (LOD) at 0.23 µM, a wide linear range (2.05–629 µM), and significant sensitivity. Therefore, the CePO4@f-CNF nanocomposite was used to study the real-time detection in chicken and fish samples, and it depicted significant results.