This study has been carried out to develop a novel magnetic separator which uses alternating magnetic field to exploit dissimilarities in electromagnetic properties of minerals. The alternating magnetic field imparts rotational movement in a free-falling hematite particle to enhance particle deflocculation and it also produces repulsive force on semiconductive pyrolusite and diamagnetic quartz particles to improve separation efficiency. A mathematical model has been developed using first principal modelling and C++ programming language to simulate trajectories of different mineral (hematite & pyrolusite) particles of diverse sizes (0.5, 1, 3 mm) under variable magnetic field intensities (5–7 K gauss) and at different rotation speed (15, 25, 30 rpm) of magnetic roll. A magnetic separator of 10 kg/h has been designed and fabricated using the modelling results and setup has been tested using different size steel balls to validate the idea. Real time applicability of the system is tested using ferruginous manganese ores (25.6–43% Mn & 1.1–1.6 Mn/Fe) and results are compared with conventional magnetic separators. Experimental studies have been carried out for different feed rates and slurry densities to maximize the effect of particle rotation and repulsion to improve mineral selectivity and separation. Studies revealed that particle shape is an important parameter for axial rotation of particles and magnetic coagulation takes place to segregate the magnetic and nonmagnetic particles. The results revealed that new design rotating magnetic field separator has achieved 5 to 10.2% increment in Mn % & 0.4-to-0.7-unit increment in Mn/Fe ratio to produce a concentrate (nonmagnetic product) of 35.8–48% Mn & 1.6–3.3 Mn/Fe. It was found that developed equipment can attain higher selectivity index compared to conventional magnetic separators. These studies have shown that the developed magnetic separator has a potential to improve the efficiency of existing magnetic separation process as well as its application can be explored for other multi-magnetic mineral materials such as electronic waste, ilmenite, chromite, etc.