The rapid growth in the number of electric bicycles (e-bicycles) has greatly improved daily commuting for residents, but it has also increased traffic collisions involving e-bicycles. This study aims to develop an autonomous emergency braking (AEB) system for e-bicycles to reduce rear-end collisions. A framework for the AEB system composed of the risk recognition function and collision avoidance function was designed, and an e-bicycle following model was established. Then, numerical simulations were conducted in multiple scenarios to evaluate the effectiveness of the AEB system under different riding conditions. The results showed that the probability and severity of rear-end collisions involving e-bicycles significantly decreased with the application of the AEB system, and the number of rear-end collisions resulted in a 68.0% reduction. To more effectively prevent rear-end collisions, a low control delay (delay time) and suitable risk judgment criteria (TTC threshold) for the AEB system were required. The study findings suggested that when a delay time was less than or equal to 0.1 s and the TTC threshold was set at 2 s, rear-end collisions could be more effectively prevented while minimizing false alarms in the AEB system. Additionally, as the deceleration rate increased from 1.5 m/s² to 4.5 m/s², the probability and average severity of rear-end collisions also increased by 196.5% and 42.9%, respectively. This study can provide theoretical implications for the design of the AEB system for e-bicycles. The established e-bicycle following model serves as a reference for the microscopic simulation of e-bicycles.