Objective To develop core competencies for learning health system (LHS) researchers to guide the development of training programs. Data Sources/Study Setting Data were obtained from literature review, expert interviews, a modified Delphi process, and consensus development meetings. Study Design The competencies were developed from August to December 2016 using qualitative methods. Data Collection/Extraction Methods The literature review formed the basis for the initial draft of a competency domain framework. Key informant semi‐structured interviews, a modified Delphi survey, and three expert panel (n = 19 members) consensus development meetings produced the final set of competencies. Principal Findings The iterative development process yielded seven competency domains: (1) systems science; (2) research questions and standards of scientific evidence; (3) research methods; (4) informatics; (5) ethics of research and implementation in health systems; (6) improvement and implementation science; and (7) engagement, leadership, and research management. A total of 33 core competencies were prioritized across these seven domains. The real‐world milieu of LHS research, the embeddedness of the researcher within the health system, and engagement of stakeholders are distinguishing characteristics of this emerging field. Conclusions The LHS researcher core competencies can be used to guide the development of learning objectives, evaluation methods, and curricula for training programs.