Anxiety towards research among post-graduate students is an increasing concern, prominently affecting research productivity, academic performance and the overall mental health of the students. Therefore, this study aimed to assess levels of anxiety toward research and associated factors among postgraduate students at Jimma University Institute of Health, southwest Ethiopia. An institutional-based cross-sectional study was conducted from May 20 to June 20, 2024. The study was conducted among 422 postgraduate students selected by stratified random sampling method. Data was collected through a pretested online survey on Google forms. The collected data were checked, cleaned, and coded in Microsoft Excel and then exported to SPSS version 26 for analysis. A multivariable logistic regression analysis was conducted to analyze the association between dependent and independent variables. The associated factors were declared at p-value < 0.05 with AOR at 95% confidence interval (CI). From the total sampled students, 407(96.44%) were respondents in this study and 232 (57%; 95% CI: 52%, 62%) were reported to have a high research anxiety level. Being female (AOR = 6.54), those in MSc/MPH programs (AOR = 4.53), low research self-efficacy (AOR = 2.18), weak supervision quality (AOR = 2.76) and poor research infrastructure (AOR = 10.21) were significantly associated with high research anxiety level. This study shows a high research anxiety level among postgraduate students and factors such as demographic factors, research self-efficacy, supervision quality, and research infrastructure were significantly associated with student’s anxiety level. Providing targeted support for female students, enhancing self-efficacy, improving supervision quality, and strengthening research infrastructure, are essential for reducing research anxiety and promoting academic success.