Brain dysfunction can be treated by restructuring neural pathways in the brain. A desired area in the brain to form a new neural pathway is selected. The area receives a sequential combination of (1) transcranial photobiomodulation therapy (PBMT) including a series of pulses having a frequency matched to a target brain wave and (2) another transcranial stimulation (e.g., transcranial direct current electrical stimulation and/or transcranial magnetic stimulation). The different stimulation mechanisms ensure that neuroplasticity occurs to restructure a neural pathway that is dysfunctional in nature to a new neural pathway that conducts normally.