Background: Puumala virus infection or nephropathia epidemica (NE) is common in northern Sweden. NE causes haemorrhagic fever with renal syndrome. Most patients make a full recovery, but a convalescent phase with fatigue has been reported. Although post-infectious fatigue has been demonstrated for other viral infections, it is not well studied in relation to NE. This study assessed recovery time and levels of fatigue in former NE patients, as compared to the general population. Methods: NE patients diagnosed in northern Sweden between 2007 and 2011, together with a comparison sample from the general population, answered a questionnaire on demographic and health-related factors, including the Fatigue Severity Scale (FSS), and characteristics of NE infection. Self-reported recovery time was assessed, and fatigue levels were compared across the two groups by multiple linear regression, stratified by gender. Results: In total, 1132 NE patients and 915 comparison group subjects participated. Time to complete recovery was reported to exceed 3 months for 47% and 6 months for 32% of the NE patients. Recovery time differed by gender and age. NE patients had significantly higher FSS scores than the comparison group. Differences were greater among women than men, and adjustments for current illness, body mass index, smoking and current residence only slightly modified the estimates. Conclusions: Individuals with previous NE infection show higher fatigue scores than non-infected individuals, even 5 years following the infection. Full recovery takes half a year or longer for a substantial proportion of former NE patients.