During his scientific career Jiří Wackermann authored or co-authored about eighty original communications in refereed journals, numerous contributions to conference proceedings, and chapters in edited volumes. His research activities have covered several scientific disciplines:

Neurophysiology and electrophysiology of the brain

• Non-linear methods in studies of the brain's electrical activity
• State-space approach and global descriptors of EEG
• Identification of functional microstates of the brain

Psychophysiology and consciousness research

• Experimentally induced altered states of consciousness

Psychophysics and perception science

• Time perception and the metrics of "subjective time"
• Geometry of the visual field and "geometric–optical illusions"

Philosophical aspects of science

• Foundational issues in psychophysiology and psychophysics