The study aims at the Fourier spectra of an antibiotic exposed to a high-intensity pulsed magnetic field. The applied frequency was f = 40 kHz, with a number of pulses n = 1, at intensities of the pulsed magnetic field H = 0.09 × 106 А/m, Н = 0.50 × 106 А/m, Н = 0.82 × 106 А/m. It was assumed that under the conditions of the pulsed magnetic field there might be a change in the structure of the drug molecule. The research has revealed that an increase in the pulsed magnetic field power leads first to a decrease in the intensity of the band in the Fourier spectrum, and then to its increase. In addition, changes were recorded in the amide group of benzylpenicillin sodium salt molecules depending on the intensity of the pulsed magnetic field applied to the antibiotic.