University research centers must manage projects for technological research that broadens the knowledge frontier as well as deal with industrial partners to foster entrepreneurship and always plan deliveries demanded by funding agencies. The literature addresses the necessity of project management skills and methods to minimize challenges. However, few studies bring the perceptions of the internal stakeholders. This paper analyzed and raised the main challenges of project management in one research center using the Current Reality Tree method through a case study. As a result, it was possible to verify three leading root causes of difficulties on project management, planning and controlling, and communication with funding agencies.