Background: The National Youth Service Corps (NYSC) is a compulsory one-year programme for graduates of tertiary schools including doctors. This study was conducted to explore the perceived benefits and challenges of serving corps medical doctors. The study would influence policy making so as to improve the experiences of corps medical doctors and help NYSC to achieve its objectives.Methods: A descriptive cross-sectional survey was conducted among 399 medical doctors doing their compulsory national youth service in Nigeria. The research instrument was developed by the researchers and pretested before use. The data obtained was analyzed using descriptive statistics and chi-square test using p < 0.05. Results: The majority (83.5%) of respondents believed that the scheme offers one or more benefits to corps medical doctors. These include Exposure to new culture (47.6%), Gaining of medical/surgical skills (36.3%) and finding lover/spouse (4.5%). Similarly, most of respondents (89.2%) reported one or more serious challenges. Some of the perceived challenges reported include; No provision of accommodation (51.6%), poor remuneration (44.7%) and exploitation (41.4%). Majority of the corps doctors expressed dissatisfaction with their job on the scheme reporting that it would have no role to play in their professional development. There was a significant association between job satisfaction and region of deployment (p-value: <0.001), gender (p-value: 0.021) and marital status (p-value: 0.008). The region of deployment and marital status were found to have a statistically significant association with the overall perceived challenges with p-value of 0.012 and < 0.001 respectively. Treatment at Places of Primary Assignment (PPAs) was mostly reported to be fair and it had a statistically significantly association with region of deployment (p-value: 0.012), location of medical school (p-value: 0.023) and gender (p-value: <0.001)Conclusions: The overall perception of NYSC among corps doctors is poor and majority have suggested that the scheme be scrapped or revamped.