AbstractSalmon‐lice have the potential to change the behaviour and growth of their salmonid host species. Here, the baseline infection levels of salmon‐lice of post‐smolts (n = 815) and veteran migrants (n = 875) of sea‐run Arctic charr (Salvelinus alpinus Linnaeus, 1758) were monitored over two successive years in a sub‐Arctic Norwegian fjord without farming of salmonids. All Arctic charr were collected after the sea‐migration period from a trap placed in the river, ascending to their overwintering freshwater habitat (Lake Laksvatn). The sea‐lice infection showed a stable infection across the 2 years while increasing through the migration period and with the size of the wild sea‐run Arctic charr. The prevalence of sea‐lice infection was intermediate to high, and the intensities of sea‐lice infections observed were generally modest, although some individuals had high infections. The relatively high infection of salmon‐lice highlights the potential detrimental effects these parasites can have at both the individual and population level of such endangered sub‐Arctic life‐history strategies. A comparative study should be performed in fjords with aquaculture activity as focal points for salmon‐lice, to investigate the impact farming have on sea‐run Arctic charr populations.