Abstract Background Pemphigus is an autoimmune bullous disease (AIBD) and has two main subtypes, pemphigus vulgaris (PV) and pemphigus foliaceus (PF). For adequate interpretation and comparison of clinical studies in pemphigus, it is essential to have outcomes and outcome measurement instruments (OMIs) that are well-defined, uniform and relevant. Objectives To provide a comprehensive overview of previously reported outcomes and OMIs in pemphigus clinical research over the past two decades. Methods A systematic literature search was performed in the databases MEDLINE, Embase, CINAHL, PsycINFO, Cochrane CENTRAL, Web of Science and trial registries covering the period between January 2002 and December 2023. Clinical trials, prospective cohort studies and systematic reviews were included. Retrospective studies were excluded. All identified outcomes and their respective OMIs were grouped into outcome domains and areas. Results From all the included studies (n = 205), a total of 1502 outcomes were extracted verbatim, categorized in 55 outcome domains and 11 outcome areas. We found a gradual increase in the number of published trials over the past two decades. The included studies mainly focused on ‘clinical response’ (92%), ‘safety monitoring’ (75%) and ‘immune response’ (61%). ‘Quality of life’ was sparsely reported (12%). Heterogeneity of reported outcomes was observed across all study designs. Within the outcome area ‘clinical response’, the proportion of defined outcomes based on the 2008 consensus statement has not been consistent over time. However, four recent clinical trials used primary endpoints based on the 2008 consensus definitions. Moreover, a broad spectrum of outcome measurement instruments (n = 65) was reported. Conclusions This review showed a wide variety in reported outcomes and OMIs in pemphigus clinical research over the past two decades. Despite standardization efforts, most studies still lack well-defined, consistent and relevant outcomes and OMIs. However, a positive trend is emerging as four recent trials did use consensus-based definitions and patient-focused OMIs. Nevertheless, the outcomes are overly stringent, lack patient-centeredness, and do not include intermediate endpoints. Therefore, refinement of the 2008 expert consensus statement through collaborative efforts of all stakeholders is essential to promote uniformity in future pemphigus outcome measurement and to advance pemphigus drug development.