Background: Watching three-dimensional television (3D TV) may strain the eyes. However, other potential harmful effects of 3D TV watching have been rarely investigated. The current study examined the impact of 3D TV watching on neurophysiological responses and cognitive functioning as compared with two-dimensional TV (2D TV) watching. Methods: A total of 72 individuals were randomly assigned to either a 3D TV watching group or a 2D TV watching group. Electroencephalography (EEG) was used to measure neurophysiological responses, and computerized neurocognitive tests were conducted immediately before and after TV watching. The Simulator Sickness Questionnaire (SSQ) was used to assess visual discomfort. Results: There was a significant change in visual discomfort between the two groups (SSQ score at baseline: 2.28 ± 3.05 for the 3D TV group and 3.69 ± 3.49 for the 2D TV group; SSQ score after watching TV: 4.6 ± 3.35 for the 3D TV group and 4.03 ± 3.47 for the 2D TV group), and this change was greater for the 3D TV watching group (P = 0.025). However, 3D TV watching did not have a differential impact on EEG responses. Furthermore, there were no significant differences between the groups in terms of changes in cognitive performance, except for a subtle difference in backward digit span performance. Conclusion: Our findings suggest that 3D TV watching is as safe as 2D TV watching in terms of neurophysiological responses and cognitive functioning. Potential harmful effects of TV viewing might be similar regardless of whether 3D or 2D TV is viewed.