Currently, the only effective and commercially used treatment for amoebic gill disease (AGD) in farmed Tasmanian Atlantic salmon is freshwater bathing. Hydrogen peroxide (H2O2), commonly used throughout the aquaculture industry for a range of topical skin and gill infections, was trialled in vitro and in vivo to ascertain its potential as an alternative treatment against AGD. Under in vitro conditions, trophozoites of Neoparamoeba perurans were exposed to three concentrations of H2O2 in sea water (500, 1000 and 1500 mg L−1) over four durations (10, 20, 30 and 60 min) each at two temperatures (12 and 18 °C). Trophozoite viability was assessed immediately post-exposure and after 24 h. A concentration/duration combination of 1000 mg L−1 for >10 min demonstrated potent amoebicidal activity. Subsequently, Atlantic salmon mildly affected with experimentally induced AGD were treated with H2O2 at 12 and 18 °C for 15 min at 1250 mg L−1 and their re-infection rate was compared to freshwater-treated fish over 21 days. Significant differences in the percentage of filaments affected with hyperplastic lesions (in association with amoebae) and plasma osmolality were noted between treatment groups immediately post-bath. However, the results were largely equivocal in terms of disease resolution over a 3-week period following treatment. These data suggest that H2O2 treatment in sea water successfully ameliorated a clinically light case of AGD under laboratory conditions.