The present study was designed to elucidate the influence of the magnetic field on the spectroscopic characteristics of nimesulide and glucosamine sulfate preparations. The secondary objective of the study was to evaluate the clinical effectiveness of the combined application of magnetotherapy and transdermal forms containing a non-steroidal anti-inflammatory preparation and a chondroprotector with the use of magnetophoresis. For this purpose, we analyzed the samples exposed to the running magnetic field in an infrared spectrometer to elucidate the changes in the optical characteristics of the preparations of interest. The clinical effectiveness of the combined application of magnetophoresis was estimated in 83 patients presenting with knee osteoarthritis. The use of the infrared spectroscopic technique in the combination with the Fourier analysis made it possible to visualize the absence of coarse optical defects and structural changes in the test samples under the influence of the physical factors which provides the basis for their physiophoretic administration. The clinical studies conducted with the application of the combined physio-pharmacological treatment have demonstrated the feasibility and high effectiveness of this approach for the management of the patients presenting with articular pathology. The rehabilitative measures accelerated the earlier appearance of the pronounced analgesic effect and promoted the restoration of the joint function. Moreover, they reduced the drug load and improved the quality of life of the patients.