Magnetic molecularly imprinted nanoparticles were fabricated for cytidine adsorption. Molecularly imprinted polymers were prepared by complexing N-methacryloyl-l-histidine/Cu(II) and cytidine as a template molecule in a highly cross-linked polymer. Magnetic molecularly imprinted nanoparticles were tested in batch experiments with aqueous samples of cytidine, and several parameters were investigated. The N-methacryloyl-l-histidine/Cu(II) complex was selected to obtain a rebinding of cytidine on the magnetic nanoparticles. The template molecule was removed using 1.0 M NaCl as a desorption agent. The adsorption of cytidine was optimal in a buffer solution of pH 7.4 for 120 min with adsorption capacity of 39.77 mg/g. The imprinted polymer-based magnetic nanoparticles were selective toward cytidine as compared to the analogs (uridine and thymidine). The adsorption fitted a Langmuir isotherm model with an R-2 value of 0.9861 and the Q(max) value of 43.86 mg/g for the magnetic molecularly imprinted nanoparticles.