BACKGROUND: Integrated reminders within clinical systems have become more prevalent due to the use of electronic health records and evidence demonstrating an increase in compliance within practice. Clinical reminders are assessed for effectiveness on an individual basis, rather than in combination with existing prompts for other conditions. The growing number of prompts may be counter-productive as healthcare professionals are increasingly suffering from "reminder fatigue" meaning many reminders are ignored. This work will review the qualitative evidence to identify barriers and enablers of existing prompts found within computerised decision support systems. Our focus will be on primary care where clinicians have to negotiate a plethora of reminders as they deal with increasingly complex patients and sophisticated treatment regimes. The review will provide a greater understanding of existing systems and the way clinicians interact with them to inform the development of more effective and targeted clinical reminders. METHODS: A comprehensive search using piloted terms will be used to identify relevant literature from 1960 (or commencement of database) to 2017. MEDLINE, MEDLINE In Process, EMBASE, HMIC, PsycINFO, CDSR DARE, HTA, CINAHL and CPCI, will be searched, as well as grey literature and references and citations of included papers. Manuscripts will be assessed for eligibility, bias and quality using the CASP tool with narrative data being included and questionnaire based studies excluded. Inductive thematic analysis will be performed in order to produce a conceptual framework defining the key barriers around integrated clinical reminders. DISCUSSION: Indications of alert and reminder fatigue are found throughout the current literature. However, this has not been fully investigated using a robust qualitative approach, particularly in a rapidly growing body of evidence. This review will aid people forming new clinical systems so that alerts can be incorporated appropriately. SYSTEMATIC REVIEW REGISTRATION: PROSPERO: CRD42016029418.