Abstract Introduction There is a concerning trend of emigration among highly educated individuals in Montenegro. This includes medical professionals who seek better job opportunities abroad. The aim of the present study was to identify the primary motivational factors driving Montenegrin medical students to pursue a career in medicine, and whether these factors undergo changes over the course of their studies. Methods A cross-sectional study included 210 medical students in Montenegro, 27.62% were males, and 72.38% were females. The mean age of the students was 21.90 years (SD=3.05) (range 19–39). Their academic motivation was analysed using the Academic Motivation Scale, previously validated in various cultural contexts. Results The results showed that autonomous motivation levels were higher than controlled motivation levels (p<0.001) among students in Montenegro, which has been previously associated with better learning outcomes. Students with medical doctors among their family members had higher extrinsic motivation related to rewards and punishments (extrinsic motivation with external regulation p=0.018). Amotivation showed a trend of increasing as the students got closer to graduation (p=0.057). Only 8.1% of students planned a career in primary healthcare, and 1% wished to specialize in family medicine. Conclusions This study’s findings, which indicate high levels of autonomous motivation among medical students, are of significant importance. They contribute to a comprehensive understanding of the motivation factors among medical students and young healthcare professionals in Montenegro. Moreover, they provide a basis for the implementation of strategic interventions to retain highly skilled medical professionals within the country’s workforce, thereby addressing the concerning trend of emigration among this group.