Olfactory and visual sensory mechanisms seem to play a critical role in migratory orientation and navigation. How these two mechanisms are functionally linked with other migratory processes is unknown. We investigated this, in relation to the profound behavioural shift that occurs during migration in the night-migratory blackheaded bunting (Emberiza melanocephala). Photosensitive unstimulated birds singly housed in activity cages were subjected to long days (LD 16/8). The activity of each bird was continuously monitored. Daily activity pattern defined the nonmigratory phase (no nocturnal activity) and migratory phase (intense nocturnal activity, Zugunruhe). Body mass and testis size were measured at the beginning and end of the experiment. Long days induced the migratory phenotype (body fattening and Zugunruhe) and testis maturation. The c-fos (Fos) immunoreactivity, as marker of the neural activity of the olfactory and visual subsystems, was measured at midday (8 h after lights-on) and midnight (4 h after lights-off) after the first seven long days (nonmigratory phase) and after seven nights of the Zugunruhe (migratory phase). In the nonmigratory phase, Fos-like immunoreactive (Fos-lir) cells in the olfactory and visual subsystems were high in the day and low at night. In the migratory phase, this was reversed; Fos-lir cells were high at night and low in the day. The phase inversion of neural activity in the olfactory and visual systems in parallel with the behavioral shift suggests a functional coupling between the systems governing migratory flight (expressed as Zugunruhe) and migratory orientation and navigation.