Background Faecal incontinence (FI) is prevalent in 15–20% of elderly individuals and is frequently monitored in clinical trials and practice. Bowel diaries are the most common way to document FI, but, in clinical practice, are mainly used as paper-based versions. Electronic diaries (eDiaries) offer many potential benefits over paper-based diaries. The aim of this study was to develop and test an eDiary to document FI. Methods We migrated a paper FI diary to an eDiary app based on the Computer-based Health Evaluation System (CHES). To assess usability, we conducted functionality and usability tests at two time points in a sample of patients with FI. In the first assessment, the eDiary functionalities were tested, patients completed the System Usability Scale (SUS, range 0–100) and compared the paper diary with the eDiary. We set a threshold for minimum acceptable average usability at 70 points. Patients were then instructed to use the eDiary for 2 days at home and contacted to report on their usage and completed the SUS a second time. Results We recruited a sample of N = 14 patients to use the eDiary. All patients were able to use all functionalities of the eDiary and only a few patients with lower technological literacy or access to devices (n = 3) needed initial assistance. The mean usability rating given at the first time point was high with 88 points (SD 18, 95% CI 78.2–96.8) and most patients (n = 10) reported they would prefer the eDiary over the paper-based version. Nine patients (n = 9) participated in the follow-up assessment and the mean SUS rating at the second time point was 97 points (SD 7, 95% CI 92.8–100). Conclusion The eDiary showed excellent usability scores for the assessment of FI at both assessments. Generally, patients preferred the eDiary over the paper-based version. We recommend the eDiary for usage with patients who own and use a smartphone and discuss potential solutions for patients with lower technological literacy or access.