In vivo L-band electron paramagnetic resonance tooth dosimetry is a newly developed and very promising method for retrospective biodosimetry in individuals who may have been exposed to significant levels of ionizing radiation. The present study aimed to determine the relationships among enamel thickness, enamel area, and measured electron paramagnetic resonance signal amplitude with a view to improve the quantitative accuracy of the dosimetry technique. Ten isolated incisors were irradiated using well-characterized doses, and their radiation-induced electron paramagnetic resonance signals were measured. Following the measurements, the enamel thickness and area of each tooth were measured using micro-focus computed tomography. Linear regression showed that the enamel area at each measurement position significantly affected the radiation-induced electron paramagnetic resonance signal amplitude (p < 0.001). Simulation data agreed well with this result. These results indicate that it is essential to properly consider enamel thickness and area when interpreting electron paramagnetic resonance tooth dosimetry measurements to optimize the accuracy of dose estimation.