Herein, a novel ultrasensitive molecularly imprinted sensor (MIS) for selective determination of a new direct acting anti-HCV velpatasvir (VELPR) was developed and fabricated for the first time. The fabricated MIS based on modification of a glassy carbon electrode (GCE) with multi-walled carbon nanotubes-gold nanoparticles (MWCNTs-AuNPs) composite after deposition on electro-synthesized 3D starfish like hollow nickel skeleton (3D SH-Ni S) to increase conductivity and effective surface area of MIS to amplify its signal. After that, the electrode was coated with molecularly imprinted polymer (MIP) by in situ electro-polymerization forming cavity with specific affinity and natural binding sites to VELPR. Differential pulse voltammetry (DPV) was used for selective detection of VELPR in complex matrices whereas, scanning electron microscope (SEM) and cyclic voltammetry (CV) were employed to characterize the fabricated sensor. All experimental factors concerning fabrication and chemical sensing properties were carefully studied and optimized. Under the optimized variables, the fabricated sensor exhibited excellent DPV response to VELPR over the range of 0.649–80.0 ng mL−1 with LOD of 0.21 ng mL−1. In addition to high sensitivity and selectivity, the sensor response to VELPR was highly reproducible and stable. Moreover, the fabricated sensor was successfully applied for the determination of VELPR in complex biological matrices and pharmaceutical tablets.