Magnetic stimulation for neural activation is widely used in clinical and lab research. In comparison to electric stimulation using an implanted electrode, stimulation with a large magnetic coil is associated with poor spatial specificity and incapability to stimulate deep brain structures. Recent developments in micromagnetic stimulation (μMS) technology mitigates some of these shortcomings. The sub-millimeter coils can be covered with soft, biocompatible material, and chronically implanted. They can provide highly specific neural stimulation in the deep neural structure. Although the μMS technology is expected to provide a precise location of neural stimulation, the exact site of neural activation is difficult to determine. Furthermore, factors that could cause the shifting of the activation site during μMS have not been fully investigated. To estimate the location of axon activation in μMS, we first derived an analytical expression of the activating function, which predicts the location of membrane depolarization in an unmyelinated axon. Then, we developed a multi-compartment, Hodgkin-Huxley (H-H) type of NEURON model of an unmyelinated axon to test the impact of several important coil parameters on the location of axonal activation. The location of axonal activation was dependent on both the parameters of the stimulus and the biophysics properties of the targeted axon during μMS. The activating function analysis predicted that the location of membrane depolarization and activation could shift due to the reversal of the coil current and the change in the coil-axon distance. The NEURON modeling confirmed these predictions. Interestingly, the NEURON simulation further revealed that the intensity of stimulation played a significant role in the activation location. Moderate or strong coil currents activated the axon at different locations, mediated by two distinct ion channel mechanisms. This study reports several experimental factors that could cause a potential shift in the location of neural activation during μMS, which is essential for further development of this novel technology.