Numerous outbreaks of enteric red mouth disease (ERM) caused by Yersinia ruckeri O1 biotype 2 in rainbow trout farms are currently being recorded despite established vaccination procedures against this disease. This could indicate that the currently used application of single immersion vaccination (using a commercial vaccine AquaVac® RELERA™) does not provide full protection. We elucidated by a controlled duplicated experiment if different vaccine administration methods can improve level and extent of protection. Rainbow trout, Oncorhynchus mykiss were vaccinated by: (1) a single immersion in bacterin diluted 1:10 for 30 s (only primary vaccination); (2) two times 30 s immersion (primary immersion vaccination followed by booster immersion vaccination 1 month later); (3) a single i.p. injection (only primary vaccination); (4) immersion vaccination followed by injection booster 1 month later; (5) a single 1 h bath in bacterin diluted 1:2000; and (6) immersion (30 s, 1:10) plus booster (1 h in diluted 1:2000 vaccine) 5 months later). Injection challenge experiments were performed 3, 5 and 7 months post primary vaccination with 8.5 × 106 CFU/fish, 10.6 × 106 CFU/fish and 1 × 108 CFU/fish, respectively. In the first challenge trial, control fish exhibited a mortality of 76%, one time immersion vaccination had a mortality of 37%, two times immersion vaccinated fish had a 4% mortality, the one-time injection vaccinated group showed a mortality of 2% and the immersion plus injection boostered fish showed no mortality at all. When rainbow trout were challenged 5 months post primary vaccination, 26% mortality occurred in control fish, 21% in one time immersion group, 12% in two times immersion group, 5% in the one-time injection vaccinated group whereas immersion plus injection boostered fish again showed no mortality at all. When challenged 7 months post vaccination, one-time immersion vaccinated were not protected at all compared to the control group whereas injection vaccinated fish showed lower mortality (17%) compared to booster immersed fish (32% mortality) which was still better than un-vaccinated controls (44% mortality). It was noteworthy that a diluted bacterin (1:2000 for 1 h after 5 months post primary vaccination) booster showed the same effect as a booster with 1:10 bacterin dilution for 30 s applied 1 month after primary vaccination. Antibody levels showing significant elevations 28 days post challenge in vaccinated fish point to this immune parameter as a protective element. The superior and extended protection offered by booster vaccination or simply injection is noteworthy and may be applied in future vaccination strategies at farm level.