Objectives: To investigate the current status and challenges of research methodology for health promotion research (HPR), this study analyzed HPR funded by the Korea Health Promotion Foundation (KHPF) from 2005 to 2011. Methods: All of the research reports funded by the KHPF for the period were included in this study. From the literature reviewed, a framework of this study was developed. Results: Quantitative research was 67.7%. The most common quantitative research design was cross-sectional survey (46.6%). Only 7.3% of quantitative research employed theoretical frameworks, and more than a half (53.4%) used primary data. For qualitative research (2.8%), most cases were conducted together with quantitative research. No qualitative research employed a philosophical underpinning. Only 7.0% of research received consent form, and 2.1% was approved by institutional review board. The results of this study indicate that there is a need to employ various research methods to study key concepts of HPR more in-depth. Efforts should be made to reduce statistical errors and also employ newly introduced statistical methods. Conclusions: Overall, a lack of scientific evidence from the HPR reports analyzed in this study was observed. Therefore, the KHPF and the academia should work together to solve the problems indicated from this study.