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In 2010–2011, a waterborne outbreak of the parasite, Cryptosporidium hominis, affected approximately 27,000 inhabitants in the city of Östersund, Sweden. Previous research suggested that post-infectious symptoms, such as gastrointestinal symptoms and joint pain, could persist for up to 2 years after the initial infection. In this study, we investigated whether the parasite caused post-infectious sequelae for up to 5 years after the outbreak. Prospective cohort study. A randomly selected cohort of individuals residing in Östersund at the time of the outbreak was sent a postal questionnaire in 2011. Responders were sent a follow-up questionnaire in 2016 and completed items on whether they experienced a list of symptoms. We examined whether outbreak cases were more likely than non-cases to report post-infectious symptoms 5 years later. We analysed data using logistic regression and calculated odds ratios with 95% confidence intervals. The analysis included 626 individuals. Among the 262 individuals infected during the outbreak, 56.5% reported symptoms at follow-up. Compared to non-cases, outbreak cases were more likely to report watery diarrhoea, diarrhoea, swollen joints, abdominal pain, bloating, joint discomfort, acid indigestion, alternating bowel habits, joint pain, ocular pain, nausea, and fatigue at the follow-up, after adjusting for age and sex. Our findings suggested that cryptosporidiosis was mainly associated with gastrointestinal- and joint-related post-infectious symptoms for up to 5 years after the infection.