The transport of fish in aquaculture and the ornamental trade exposes fish to multiple stressors that can cause mass mortalities and economic loss. Previous research on fish transport has largely focused on chemical stress related to deterioration in water quality. Mechanical disturbance during routine fish transport, however, is unpredictable and is a neglected potential stressor when studying fish welfare. Stress induced immunosuppression, caused by mechanical disturbance can increase the chances of contracting infections and significantly increase infection burden. Here, using the model guppy–Gyrodactylus turnbulli host–parasite system and a new method of bagging fish (Breathing Bags™), which reduces mechanical disturbance during fish transport, we investigated how parasite infections contracted after simulated transport impact infection trajectories on a globally-important ornamental, freshwater species. Guppies exposed to mechanical transport disturbance suffered significantly higher parasite burden compared to fish that did not experience transport disturbance. Unfortunately, there was no significant reduction in parasite burden of fish transported in the Breathing Bags ™ compared to standard polythene carrier bags. Thus, transport induced mechanical disturbance, hitherto neglected as a stressor, can be detrimental to disease resistance and highlights the need for specific management procedures to reduce the impact of infectious diseases following routine fish transport.