Background Cancer patients are highly vulnerable to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Few studies have examined racial disparities of clinical prognosis among gastrointestinal (GI) cancer patients with COVID-19, especially after the approval of COVID-19 vaccines. Methods We conducted a retrospective study based on the University of California COVID Research Data Set (UC CORDS). Patients aged ≥ 18 with GI cancer as well as SARS-CoV-2 infection between March 10, 2020, and May 8, 2022, were included. We examined racial disparities using multivariable logistic regression. Results Among the 1054 GI cancer cases included, 117 (11.1%) patients were Asian and Pacific Islander, 51 (4.8%) were Black patients, 377 (35.8%) were Hispanic patients, 403 (38.2%) were White patients, and 106 (10.1%) belonged to other or unknown races. Fully adjusted logistic models revealed a significantly increased risk of COVID-19-related hospitalization or emergency room visits among the Black (OR = 2.26, 95% CI = 1.08–4.70), the Hispanic (OR = 2.24, 95% CI = 1.48–3.39), and the patients of other or unknown races (OR = 1.80, 95% CI = 1.00–3.26) compared with the White patients. No significant racial disparities in 30-day all-cause mortality and mechanical ventilation rate were found. Vaccination, age, cancer type, recent cancer diagnoses in UC CORDS, metastatic cancer or secondary malignant neoplasm, and Charlson comorbidity index score were associated with the prognosis of GI cancer patients with COVID-19. Conclusions GI cancer patients belonging to racial minorities experience worse COVID-19 outcomes. Vaccination status is a crucial factor associated with GI cancer patients’ prognosis among different race/ethnicity groups. Targeted communication in the context of cancer is needed to encourage vaccination uptake in this vulnerable population.