Employee turnover could affect the organisation’s performance. Job dissatisfaction and burnout have been identified as factors influencing the intention to leave. Thus, this study aimed to determine the level of intent to leave, and predictors associated with intention to leave among medical researchers in Malaysia. A cross-sectional, stratified random sampling study was conducted among researchers in a research organisation under the Ministry of Health. Respondents answered an online questionnaire that included sociodemographic information, job dissatisfaction, burnout, and intention to leave. A total of 133 researchers participated. More than one-third (41.4%) of the researchers had a moderate and high level of intention to leave. Burnout and job dissatisfaction were identified as significant predictors. Burnout was noted to have a positive relationship with the intent to leave (β = 0.289, 95% CI (B): 0.287, 1.096). Meanwhile, job satisfaction was found to have a negative relationship with the intention to leave (β = −0.348, 95% CI (B): −0.768, −0.273). Burnout among researchers is quite worrisome as more than two-thirds of the researchers experienced moderate to high burnout. Reducing burnout and job dissatisfaction would increase work performance and produce high-quality research output, hence decreasing the turnover rate.