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Background The Chinese government initiated a compulsory services programme (CSP) to provide skilled general practitioners (GPs) to rural regions. This study examined the early career trajectories of medical graduates with compulsory services and the factors influencing their retention in primary healthcare facilities.Methods A cohort of CSP graduates from four universities in central and western China was established in 2015 to examine the career development within rural healthcare settings. Annual online surveys followed up their career development. This study used baseline and follow-up data from 2015 to 2022, which involved 2041 CSP graduates. Descriptive analysis was used to report transition and job retention. Logistic regression models were used to assess factors that affect retention. Multiple chain equation imputation was employed to explore the impact of sample attrition on retention.Results After the CSP contract ended, 38.54% of the CSP graduates retained in primary healthcare facilities. Of those leaving primary healthcare, 34.65% chose hospitals above county-level, 25.41% chose county-level hospitals, 7.92% pursued higher degrees and 27.72% were unemployed. Multivariable analysis showed that signing contracts with hometown had a positive association with improved retention (OR=2.64, p=0.001). There is no significant effect of sample attrition on the retention of GPs in primary healthcare settings (p=0.247).Conclusion CSP significantly contributes to staffing rural health workforce in China. Ensuring signing contracts with hometown and lifting financial burden during school could increase retention in the long run. Increased attention should also be directed to GPs with a senior professional title to increase retention.