Aim: To describe the incidence, treatment and survival of patients with rare types of rectal malignancies in the Netherlands. Methods: Data of patients with rectal malignancies diagnosed in the Netherlands between 1989 and 2018 were retrieved from the Netherlands Cancer Registry and grouped according to the RARECARE cancer list. Age-standardised incidence rates were calculated using the European Standard Rate. The Joinpoint Regression Program was used for analysing trends and joinpoints and for the estimation of annual percentage changes (APCs). Patient characteristics, treatment details and relative survival (RS) were reported for different histological types of rectal malignancies and compared between different time periods. RS was assessed using Kaplan-Meier analysis and log-rank test. Results: A total of 88,299 cases of rectal malignancies were included of which 2125 (2.5%) were categorised as rare histological subtypes. The incidence of rectal neuro-endocrine tumours (NET) (APC: 6.2%, 95% confidence interval [CI]: 5.4%; 7.1%), rectal sarcoma (APC: 5.8%, 95% CI: 2.9%; 8.7%) and rectal adenocarcinoma (APC 1.0%, 95% CI: 0.26%; 1.8%) increased. Prognosis was best in patients with rectal NET (5-year RS: 72.4%, 95% CI: 70.1%; 74.7%) and worst in patients with rectal melanoma (5-year RS: 8.9%, 95% CI: 5.1%; 15.7%). RS has improved in patients with rectal adenocarcinoma, rectal sarcoma and rectal lymphoma in 2008–2018 (p-values p < 0.001, p = 0.023 and p = 0.029). Conclusion: Significant increases in incidence were observed for different types of rectal malignancies. Differences in incidence, treatment and survival found in this study could be useful to make clinicians aware of specific diseases.