Background: Substance use disorders (SUDs) remain a prevalent public health issue characterized by a substantial disease burden and high relapse rates. The aim of this planned project is to investigate the optimal electrode placement and polarity of transcranial direct current stimulation (tDCS) to reduce cognitive deficits and substance craving in individuals with SUDs, thereby contributing to improved treatment outcomes, including longer abstinence periods and reduced substance use after relapse. Methods: This paper is a study protocol for a planned study. The study will enroll 162 treatment-seeking individuals aged 18 to 65 years who meet the DSM-5 criteria for alcohol use disorder (AUD), including those with other comorbid SUDs. Besides receiving treatment as usual (TAU), study participants will be randomly assigned to one of six groups: anodal stimulation over right dorsolateral prefrontal cortex (DLPFC; Group 1), left DLPFC (Group 2), or lateral occipital cortex (Group 3); sham tDCS (Group 4); computerized inhibition training (Group 5); or TAU only (Group 6). Assessments will be conducted at baseline (T1), across the directly following investigation days (T2-T4), post-intervention (T5), and at four follow-ups (after 4, 8, 12 and 24 weeks) at the Central Institute of Mental Health (Mannheim, Germany) and at the Psychiatric Center Nordbaden (Wiesloch, Germany). The primary outcomes include changes in craving and inhibitory control measured through a neuropsychological task (modified Go/No-Go task), as well as changes in electroencephalogram (EEG) activity during this task, specifically in event-related potentials including the N200 and P300 components. Secondary outcomes include abstinence days and amount of alcohol consumed. Discussion: Following the completion of this study, findings from this research could inform future therapeutic strategies for SUD, potentially advancing and complementing SUD treatment approaches by integrating tDCS as a potential relapse prevention strategy. Addressing potential challenges such as participant discomfort and high dropout rates through comprehensive support is vital for the success of this study. Trial registration: Registered at https://clinicaltrials.gov/study/NCT06959342 (Date 26.04.2025).