ObjectiveMental health complaints are prevalent among people with epilepsy, yet there are major barriers that prevent access to psychological care, including high out‐of‐pocket costs and a lack of accessible specialized services. The purpose of the current study is to examine the comparative efficacy, acceptability, cost‐effectiveness, and long‐term outcomes of a digital psychological intervention when delivered under two models of care (i.e., guided vs. unguided) in supporting the mental health and functioning of adults with epilepsy.MethodApproximately 375 participants across Australia will be enrolled. Eligible participants will have a confirmed diagnosis of epilepsy, experience difficulties with their emotional health, be at least 18 years of age, and live in Australia. Participants will be randomized (2:2:1) to receive the Wellbeing Neuro Course, a 10‐week internet‐delivered program, with (i.e., guided) or without guidance by a mental health clinician (i.e., unguided), or be allocated to a treatment‐as‐usual waiting‐list control group. Participants will complete online questionnaires at pre‐, post‐treatment, and 3‐ and 12‐month follow‐up and consent to have their data linked to their medical records to capture healthcare system resource use and costs.AnalysisPrimary outcome measures will be symptoms of depression and anxiety. A cost‐utility analysis will be undertaken using the Australian healthcare system perspective and according to current economic evaluation guidelines. Resource use and costs to the healthcare system during the study period will be captured via data linkage to relevant administrative datasets in Australia.SignificanceThe results of this trial will provide important data concerning the relative outcomes of these different models of care and will inform the integration of digital psychological interventions translation into healthcare services.Ethics and DisseminationThe Human Research Ethics Committee of Macquarie University approved the proposed study (Reference No: 520231325151475). The results will be disseminated through peer‐reviewed publication(s).ANZCTR Trial Registration NumberACTRN12623001327673.Plain Language SummaryThis study seeks to find out if a 10‐week online psychological treatment can improve the mental health and well‐being of Australian adults with epilepsy. Around 375 participants will be randomly assigned to different groups: one will receive treatment with guidance from mental health clinician (guided group), one without guidance (unguided group), and one starting later (waiting control group). All participants will fill out the same outcome measures online. The main goal of this research is to compare these groups and assess how well the treatment works in improving mental health outcomes.