Brain Computer Interface (BCI) studies have been done to help people manipulate electronic devices in a 2D space but less has been done for a vigorous 3D environment. The purpose of this study was to investigate the possibility of applying Steady State Visual Evoked Potentials (SSVEPs) to a 3D LCD display. Eight subjects (4 females) ranging in age between 20 to 26 years old participated in the experiment. They performed simple navigation tasks on a simple 2D space and virtual environment with/without 3D flickers generated by a Flim-Type Patterned Retarder (FPR). The experiments were conducted in a counterbalanced order. The results showed that 3D stimuli enhanced BCI performance, but no significant effects were found due to the small number of subjects. Visual fatigue that might be evoked by 3D stimuli was negligible in this study. The proposed SSVEP BCI combined with 3D flickers can allow people to control home appliances and other equipment such as wheelchairs, prosthetics, and orthotics without encountering dangerous situations that may happen when using BCIs in real world. 3D stimuli-based SSVEP BCI would motivate people to use 3D displays and vitalize the 3D related industry due to its entertainment value and high performance.