Host behaviour can prevent infection and moderate the fitness of parasites. Antiparasite behaviours are prevalent in many host–parasite systems and occur over fine or broad scales. With global growth in aquaculture production and the associated proliferation of parasites in farming systems, the behaviour of the fish being farmed has seldom been investigated in relation to parasites. Epidemics and outbreaks of parasites are prevalent in most aquaculture systems, and behaviour could be harnessed in concert with current methods to prevent and control parasites and pathogens. However, this requires a systematic understanding of the behaviours of hosts, their capacity for resistance and their interaction with the environment and the parasite. Herein, we present evidence for how behaviour could be used in aquaculture, and discuss the possibility for behaviour to be used in aquaculture as (i) an indicator of welfare status, (ii) a tool in prevention or control and (iii) to maintain or improve welfare. We apply this framework to a case study of a highly problematic parasite, the salmon louse (Lepeophtheirus salmonis), on farmed Atlantic salmon (Salmo salar). We present the current state of the system, and the drawbacks of current control or prevention methods. We synergise current knowledge on host behaviours and show how behaviour could be incorporated into current and new approaches for prevention and control. Through this first evaluation of the possibilities behaviour presents in disease management, we aim to facilitate a shift in the current disease control paradigm from reactive‐based post‐infection control to pre‐infection prevention approaches.