In micro-organisms, as well as in metazoan cells, cellular polarization and directed migration are finely regulated by external stimuli, including mechanical stresses. The mechanisms sustaining the transduction of such external stresses into intracellular biochemical signals remain mainly unknown. Using an external magnetic tip, we generated a magnetic field gradient that allows migration analysis of cells submitted to local low-intensity magnetic forces (50 pN). We applied our system to the amoeba Entamoeba histolytica. Indeed, motility and chemotaxis are key activities that allow this parasite to invade and destroy the human tissues during amoebiasis. The magnetic force was applied either inside the cytoplasm or externally at the rear pole of the amoeba. We observed that the application of an intracellular force did not affect cell polarization and migration, whereas the application of the force at the rear pole of the cell induced a persistent polarization and strongly directional motion, almost directly opposed to the magnetic force. This phenomenon was completely abolished when phosphatidylinositol 3-kinase activity was inhibited by wortmanin. This result demonstrated that the applied mechanical stimulus was transduced and amplified into an intracellular biochemical signal, a process that allows such low-intensity force to strongly modify the migration behavior of the cell.