Aim Cardiothoracic surgery has the potential to improve care in resource-deprived countries like Nigeria. This study analyzes the barriers to training in cardiothoracic surgery and gaps in the existing curriculum from a cardiothoracic surgery trainee perspective. Methods An online nationwide mixed-method cross-sectional survey was conducted. The participants were from a pool of senior residents in cardiothoracic surgery. A five-point Likert scale was utilized to rate and evaluate their training experiences. The motivations for choosing cardiothoracic surgery, gaps in the training curriculum, perceived barriers, and facilitators in their training programs were also assessed. The survey included closed and open-ended questions to capture quantitative data and qualitative insights. The quantitative data were analyzed using SPSS 21 (Armonk, NY: IBM Corp), while the qualitative data were analyzed using MAXQDA 24 (Berlin, Germany: VERBI Software). Results Sixteen senior cardiothoracic surgery residents completed the survey. Thematic grouping identified several key barriers, such as low case volume, lack of infrastructure and equipment, and reduced trainee autonomy during cases. The significant deficiencies in the existing curriculum are the absence of clear minimum competencies, lack of local and international collaboration, and robust cardiac training. In low-resource settings like Nigeria, government participation and improved funding, increased collaboration between local and international programs, and establishment of regional centers may offer solutions and successful implementation of cardiothoracic surgery training and improve access to surgical care. Conclusion Cardiothoracic trainees are highly interested in their training despite several barriers. Increased funding, collaboration, and infrastructure development will help improve the training experience.