Abstract: BACKGROUND: Screening for gastrointestinal (GI) cancers, specifically colorectal cancer (CRC) and hepatocellular carcinoma (HCC), is often inadequately and inequitably implemented, leading to preventable morbidity and mortality. This protocol paper describes a study designed to compare the effectiveness of external facilitation with patient navigation across hospitals in the Veterans Health Administration (VA). METHODS: Two hybrid type 3, cluster-randomized trials will compare the effectiveness of patient navigation versus external facilitation for supporting HCC and CRC screening completion. Twenty-four sites will be included in the HCC trial and 32 in the CRC trial, cluster-randomizing Veterans by their site of primary care. The primary outcome of reach of cancer screening completion will be measured after intervention and during sustainment. Multi-level implementation determinants (i.e., barriers and facilitators), preconditions, and moderators will be evaluated pre- and post-intervention, using Consolidated Framework for Implementation Research (CFIR)-mapped surveys and interviews of Veteran participants and provider participants. DISCUSSION: Comparing findings in the two trials will allow researchers to understand how implementation barriers and strategies operate differently for a one-time screening in a relatively healthy population (CRC) vs. repeated screening in a more medically complex population (HCC). TRIAL REGISTRATION: This project was registered at ClinicalTrials.Gov (NCT06458998) on 6/13/24.