Population movement is a major driver for infectious disease transmission and can impact the success of disease control and elimination strategies. The relationship between disease transmission and permanent migration is well documented, but fewer studies have considered how different types of population mobility affects disease transmission and control programmes. This qualitative study was conducted on two islands of the Bijagós archipelago, Guinea Bissau to understand spatial and temporal population movement, and reasons for these movements, within, between and away from the Bijagós islands. Data were collected on two islands using key informant interviews (n = 8), daily activity-location interviews (n = 30) and focus group discussions (n = 6). Data were analysed thematically using an adapted typology of mobility. Findings revealed that movement within and between islands, and from islands to the mainland, was a common feature of island life for men and women alike. It was usual for trips away from home to last for several months at a time. Five key reasons for travel were identified: subsistence activities; family events; income generating activities; cultural festivities and healthcare. These movements often occurred erratically all year round, with the exception of seasonal travel within and between islands for agricultural purposes. Our study characterised detailed patterns of human mobility in the Bijagós islands as a first step towards understanding the potential impact of different types of mobility on disease exposure, transmission and public health programmes. Short-term mobility may have a significant impact on the spread of infectious diseases with short incubation periods. Predictable movements, such as travel for seasonal agricultural work, should be taken into account for tailoring and increasing the reach of public health interventions. Further research is needed to understand the role of human behaviour and mobility in disease transmission and control across the archipelago.