The elevated level of very-low-density lipoprotein (VLDL) in the blood is associated with coronary heart disease; therefore, its detection is of significant clinical importance. In this work, molecularly imprinted polymer (MIP) layers fabricated with ZnO nanoparticles are developed for gravimetric sensing of VLDL. The use of methacrylic acid (MAA) and β-cyclodextrin (β-CD) as functional co-monomers in an optimized ratio of 1:1 for MIP synthesis controls the hydrophilicity/hydrophobicity; thus, yielding highly tailored recognition sites having adequate stability. The as-prepared ZnO nanoparticles are characterized by scanning electron microscopy (SEM), Fourier transformation infrared (FTIR), and X-ray diffraction (XRD) before incorporating into the MIP matrix. The template concentration in MIP is also varied to select its optimal amount, i.e., 50 µL of 50 µg/mL VLDL solution for enhanced sensor performance. Sensor measurements reveal that the ZnO-MIP has a sensitivity of 19.285 Hz.ng-1mL-1 for VLDL, which is about 16-fold higher than the reference ZnO-NIP (non-imprinted polymer) channel. Furthermore, the ZnO-MIP sensor exhibits high selectivity for VLDL as the sensor response is 6 and 3 times higher compared to α1-acid glycoprotein and human serum albumin (HSA), respectively. Finally, the performance of the developed sensor setup is evaluated for the detection of VLDL in human serum samples indicating its potential for reliable analysis of VLDL in complex biofluids.