The main research area of Parkkonen is non-invasive neuroimaging, mainly instrumentation and data analysis methods related to MEG as well as human neuroscience of sensory modalities and cognition. He has contributed to MEG instrumentation and signal processing methods that are currently in active use in over 100 laboratories world-wide. Currently he pursues the use of optically-pumped magnetometers for MEG, exploits real-time feedback of measurements of brain activity to study cognition and plasticity, both for basic neuroscientific research and for clinical applications. He is also coordinating a national consortium to develop a biobank for functional brain-imaging data.

Parkkonen has also contributed to ultra-low-field MRI research and to invasive monitoring of local cortical activity. In cognitive neuroscience, Parkkonen has shed light on the neural mechanisms of sensory processing, particularly conscious visual perception. Recently he has pioneered the emerging field of social neuroscience to uncover brain mechanisms supporting social interaction by using hyperscanning i.e. simultaneous recording of the brain activity of the interacting participants.