Background Endoscopic resection for early oesophageal cancer was introduced around 2000 in the Netherlands. The scientific question was how the treatment and survival of early oesophageal and gastro-oesophageal junction cancer has changed over time in the Netherlands. Methods Data were obtained from the nationwide population-based Netherlands Cancer Registry. All patients diagnosed with clinical in situ or T1 oesophageal or GOJ cancer without lymph node or distance metastasis during the study period (2000–2014) were extracted. Primary outcome parameters were the trends in treatment modalities over time and relative survival of each treatment regime. Results A total of 1020 patients were diagnosed with a clinical in situ or T1 oesophageal or gastro-oesophageal junction cancer without lymph node or distance metastasis. The proportion of patients who received endoscopic treatment increased from 2.5% in 2000 to 58.1% in 2014. During the same period the proportion of patients who received surgery decreased from 57.5 to 23.1%. Five-year relative survival of all patients was 69%. Five-year relative survival after endoscopic therapy was 83% and after surgery 80%. Relative excess risk analyses showed no significant difference in survival between patients in the endoscopic therapy group and patients in the surgery group after adjustment for age, sex, clinical TNM classification, morphology and tumour location (RER 1.15; CI 0.76–1.75; p 0.76). Conclusion Our results demonstrate an increase in endoscopic treatment and a decrease of surgical treatment for in situ and T1 oesophageal/GOJ cancer between 2000–2014 in the Netherlands. The relative 5-year survival after endoscopic treatment is high (83%) and comparable with surgery (80%).