Background Healthcare access and outcomes in cancer patients with schizophrenia remain unclear. Aims To investigate the likelihood of early diagnosis and treatment in patients with schizophrenia who have cancer and their prognosis. Method A retrospective matched-pair cohort of gastrointestinal cancer patients was identified using a national in-patient database in Japan. Multivariable ordinal/binary logistic regressions was modelled to compare cancer stage at admission, invasive treatments and 30-day in-hospital mortality between patients with schizophrenia (n = 2495) and those without psychiatric disorders (n = 9980). Results The case group had a higher proportion of stage IV cancer (33.9% v. 18.1%), a lower proportion of invasive treatment (56.5% v. 70.2%, odds ratio (OR) = 0.77, 95% CI 0.69-0.85) and higher in-hospital mortality (4.2% v. 1.8%, OR = 1.35, 95% CI 1.04-1.75). Conclusions Patients with schizophrenia who had gastrointestinal cancer had more advanced cancer, a lower likelihood of invasive treatment and higher in-hospital mortality than those without psychiatric disorders.