This study on the epidemiology of banana bunchy top disease (BBTD) was carried out in the context of small-scale farms in Burundi for an integrated management approach. Banana trials were established in farmers’ fields comparing different plot locations, while spatial and seasonal occurrence of aphid vectors was evaluated at three different altitudes. In addition, serological tests were performed on banana leaf samples to confirm the presence and titre of the virus. The results showed that BBTD incidence varied among banana cultivars and locations. Nine months after plot establishment, BBTD incidence ranged from 21·8% to 56·4% in plots within affected fields, while a range of 0–12·3% was reported in plots located between 5 and 30 m away from affected banana fields. Aphid numbers were highest in the dry season. These aphids were able to acquire and transmit the virus irrespective of altitude. A mean incubation period of 21 and 84 days was observed at low (780 m a.s.l.) and high (2090 m a.s.l.) altitude, respectively. Thus, a holistic approach, taking into account banana cultivar, plot location, disease-free planting material and regular field sanitation, should be promoted for long-term BBTD management.