Background: Central African countries have an increasing burden of disease, low specialist workforce densities, and under-resourced postgraduate medical education. The residency program choice of today’s medical students will determine specialist workforce density in the near future. This study aims to elucidate the factors that influence the choice of residency programs among medical students of two Central African countries. Methods: We designed an online questionnaire in French and English with closed-ended, open-ended, and Likert scale questions. Links to both forms were shared via the international messaging application, WhatsApp, and data were collected anonymously for one month. Respondents were sixth- and seventh-year medical students enrolled in nine Cameroonian and Congolese schools. The threshold of significance was set at 0.05 for bivariate analysis. Results: There were 149 respondents in our study, 51.7% were female, and 79.2% were from Cameroon. Almost every student (98%) expressed the wish to specialize, and a majority (77.2%) reported an interest in a residency program abroad. Preferred destinations were France (13.7%), Canada (13.2%), and the U.S.A. (11.9%). The most popular specialties were cardiology (9.4%), pediatrics (9.4%) and obstetrics and gynecology (8.7%). The choice of specialty was made based on the respondent’s perceived skills (85.9%), anticipated pay after residency (79.2%), and patient contact (79.2%). Conclusion: Understanding which specialties interest Cameroonian and Congolese medical students and the reasons for these choices can help develop better local programs.