A wireless EEG-based brain-computer interface (BCI) and an FPGA-based system to control electric wheelchairs through a Bluetooth interface was proposed in this paper for paralyzed patients. Paralytic patients can not move freely and only use wheelchairs in their daily life. Especially, people getting motor neuron disease (MND) can only use their eyes and brain to exercise their willpower. Therefore, real-time EEG and winking signals can help these patients effectively. However, current BCI systems are usually complex and have to send the brain waves to a personal computer or a single-chip microcontroller to process the EEG signals. In this paper, a simple BCI system with two channels and an FPGA-based circuit for controlling DC motor can help paralytic patients easily to drive the electric wheelchair. The proposed BCI system consists of a wireless physiological with two-channel acquisition module and an FPGA-based signal processing unit. Here, the physiological signal acquisition module and signal processing unit were designed for extracting EEG and winking signals from brain waves which can directly transformed into control signals to drive the electric wheelchairs. The advantages of the proposed BCI system are low power consumption and compact size so that the system can be suitable for the paralytic patients. The experimental results showed feasible action for the proposed BCI system and drive circuit with a practical operating in electric wheelchair applications.