Aim Nurses have the potential to perform fiberoptic endoscopic evaluation of swallowing (FEES) in Japan, which can aid in their provision of swallowing care appropriate to individual patients' swallowing functions. We aimed to confirm the safety and effectiveness of a new nursing education program on FEES by examining its impact on autonomy in performing FEES and accuracy in observing bolus swallowing. Methods In this prospective descriptive study, we developed a FEES education program comprising three phases: (a) obtaining knowledge and skills through e-leaning and a practical workshop; (b) becoming proficient in skills for assessing healthy adults through self-learning; and (c) obtaining clinical competence through 30 cases of on-the-job training (OJT). The trends in autonomy and in accuracy of FEES were evaluated by the data during OJT. Results Of the three certified nurses in dysphagia nursing, a trainee completed 30 cases of OJT and the other two trainees experienced 20 cases and 10 cases, respectively without any adverse event. Autonomy in the four major FEES skills gradually increased over the OJT. The correct answer rate, sensitivity, and specificity of the penetration-aspiration scale and severity of residue in the pyriform sinus and epiglottis valley were above 95% at the first 10 cases of OJT among three trainees and they were 100% after the 11th case of OJT. Conclusions Our results suggest that the developed education program helped nurses with experience being present at FEES obtain sufficient knowledge and skills to appropriately and safely perform FEES with 30 cases of OJT.