Background: Gastrointestinal stromal tumours (GIST) are rare malignant mesenchymal tumours with an incidence of 1 in 100,000. They represent only 5% of gastrointestinal tumours. The GISTs are mainly located in the stomach (60–70%) and in the rectum in < 5% of cases. In the case of localized, resectable tumours, the treatment is surgical resection. Depending on the size and localization of the tumour in the rectum, either a local excision, rectal resection with anastomosis, or abdominoperitoneal amputation with permanent stoma can be performed. In contrast to carcinomas, the metastasis of GISTs into lymph nodes is rare; therefore, from an oncological point of view, lymphadenectomy in the form of mesorectal excision is not required. Neoadjuvant treatment using tyrosine-kinase inhibitors (TKI) is recommended for tumours larger than 5 cm and in case of tumours infiltrating surrounding organs or sphincters in order to achieve complete resectability, less mutilating and continent procedure. In GISTs with a positive resection line, re-resection can be attempted. Adjuvant TKI therapy can be considered in cases of CD117 positivity and after resections of GISTs with medium and high-risk malignant behaviour. The TKI treatment is also indicated in cases of unresectable and metastatic GISTs. Methods: Data obtained from the GIST registry by the 1st January 2017, when 10 centres in the Czech Republic were contributing to the registry, were analysed. Results: We analysed 1,095 patients out of which 45 (4.1%) had GIST localized in the rectum. The average age of the patients was 60 years. There were significantly more males (68.9%; p = 0.0007) and symptomatic patients (62.2%; p = 0.034). In total, 82% of the patients underwent surgery. Local excision was performed in 37.8%, resection of the rectum with anastomosis in 29.7%, and Miles operation in 29.7%. In the cohort, most tumours were 2–5 cm in size and almost half of the tumours presented a high risk of malignant behaviour. Systemic treatment was reported in 73% of patients. A complete remission was achieved in 80% of patients with GIST of the rectum. The median survival rate was 11.3 years and the 5-year survival rate is 90.6%. Conclusion: Despite the success of TKI treatment, the only potentially curative method of rectal GISTs is a surgical R0 resection. Given the relatively rare frequency of these tumours, proper diagnosis and treatment is demanding. Therefore, these patients should be preferably treated in specialised ce.