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Introduction Cryptosporidiosis is a leading cause of moderate-to-severe diarrhoea globally, and, while it is often self-limited, in immunocompromised individuals, the infection can be associated with significant morbidity and mortality. Diagnosis might be missed or delayed in patients with inflammatory bowel disease (IBD) due to similar presentation, and these patients may also be on immunosuppressive therapies, increasing their risk of infection. Additionally, gastrointestinal infection and dysbiosis may be a risk factor for IBD. Diagnosis, presentation and treatment of cryptosporidiosis in individuals with IBD, as well as any epidemiologic correlations between the two diseases, will be investigated.Methods and analysis MEDLINE, Embase, Cochrane Library, CINAHL, Dissertations and Theses Global and grey literature will be searched. Joanna Briggs Institute (JBI) methodology for scoping reviews was used for the protocol and will be for the review. Two reviewers will independently screen studies and extract data. The evidence and presentation of the results will be analysed with input from the review team. Studies of cryptosporidiosis in patients with IBD will be included. Paediatric, adolescent and adult studies in all patient environments will be included. Cases in which Crohn’s disease does not affect the intestine and cases in which cryptosporidial infection is not in the intestine will be excluded.Ethics and dissemination Published clinical literature will be systematically reviewed, and this work does not directly involve patients. Consequently, ethical review by an institutional review board is not required. Data will be presented at academic conferences, and a culminating report will be published in a peer-reviewed journal.Open Science Framework registration https://osf.io/j47mb.