Noisy human activities such as helicopter traffic may affect physiology and behaviour of wild animals. Since chronic behavioural modifications can ultimately alter reproductive success and population dynamics, studying the response of different taxa and species to human-induced disturbance in different habitats is paramount. The present study analysed data collected from 10 male Alpine ibex (Capra ibex) monitored with GPS collars to assess their response to disturbance caused by helicopter overflights. We compared ibex activity levels in the hours before and after 34 helicopter overflights during the summer of 2013 in Gran Paradiso National Park (Italy), a protected area that is essential for the conservation of Alpine ibex. The behaviour of Alpine ibex was affected both during and after helicopter overflights: compared to the average activity levels in the hours before the disturbance event, activity increased during the disturbance and decreased during the hour following the overflights. The reduction in activity persisted over the whole day of the helicopter disturbance and finally went back to normal levels during the following day. There was no evidence of habituation to the disturbance throughout the study period. The prolonged behavioural response to the disturbance suggests that frequent helicopter overflights may ultimately affect the ibex’s body conditions, as well as the life-history traits of a population. These findings highlight the importance of considering medium and long-term behavioural responses in assessing disturbance-related effects on wildlife populations.