With the aim of optimization, numerical simulations of the cooling and vacuum systems of a compact 12 MeV race-track microtron (RTM) which is under construction at the Technical University of Catalonia have been carried out. The hydraulic and thermal performance of the cool- ing system for various flow rates has been studied using the Computational Fluid Dynamics (CFD) software. A CFD model, previously validated with experimental pres- sure loss results, has permitted to simulate the cooling fluid temperature, inner wall temperatures and heat trans- fer coefficients at different sections of the RTM accelerat- ing structure. Conclusions concerning the current design and its possible optimization are discussed. Simulations of the RTM high vacuum conditions have been performed using the Monte-Carlo simulation package Molflow+. The pressure in the vacuum chamber, pumping tube con- ductance and maximum allowed throughput have been calculated. Also results of the vacuum chamber pumping out sessions are reported.