Background Human resource is one of the health system’s building blocks, which ultimately leads to improved health status, equity, and efficiency. However, human resources in the health sector are characterized by high attrition, distributional imbalance, and geographic inequalities in urban and rural settings. Methods An discrete choice experiment (DCE) with 16 choice tasks with two blocks containing five attributes (salary, housing, drug and medical equipment, year of experience before study leave, management support, and workload) were conducted. A latent class and mixed logit model were fitted to estimate the rural job preferences and heterogeneity. Furthermore, the relative importance, willingness to accept and marginal choice probabilities were calculated. Finally, the interaction of preference with age and sex was tested. Results A total of 352 (5632 observations) final-year medical students completed the choice tasks. On average, respondents prefer to work with a higher salary with a superior housing allowance In addition, respondents prefer a health facility with a stock of drug and medical equipment which provide education opportunities after one year of service with supportive management with a normal workload. Young medical students prefer lower service years more than older students. Besides age and service year, we do not find an interaction between age/sex and rural job preference attributes. A three-class latent class model best fits the data. The salary was the most important attribute in classes 1 and 3. Contrary to the other classes, respondents in class 2 do not have a significant preference for salary. Respondents were willing to accept an additional 4271 ETB (104.2 USD), 1998 ETB (48.7 USD), 1896 ETB (46.2 USD), 1869 (45.6 USD), and 1175 ETB (28.7 USD) per month for the inadequate drug and medical supply, mandatory two years of service, heavy workload, unsupportive management, and basic housing, respectively. Conclusion Rural job uptake by medical students was influenced by all the attributes, and there was individual and group-level heterogeneity in preference. Policymakers should account for the job preferences and heterogeneity to incentivize medical graduates to work in rural settings and minimize attrition.