Dimethyl Ether (DME) is considered a clean alternative fuel to diesel due to its soot-free combustion characteristics and its capability to be produced from renewable energy sources rather than fossil fuels such as coal or petroleum. To mitigate the effect of strong wave dynamics on fuel supply lines caused due to the high compressibility of DME and to overcome its low lubricity, a hydraulically actuated electronic unit injector (HEUI) with pressure intensification was used. The study focuses on high pressure operation, up to 2000 bar, significantly higher than pressure ranges reported previously with DME. A one-dimensional HEUI injector model is built in MATLAB/SIMULINK graphical software environment, to predict the rate of injection (ROI) profile critical to spray and combustion characterization. The outputs of model are compared with experimental ROI and injection duration data of both diesel and DME at injection pressures ranging from 750 to 2000 bar for single-hole and multi-hole nozzles. DME was found to have, with respect to diesel, longer injection delays leading to shorter injection durations for same injector command. The DME ROI profiles show that the volumetric flowrates are higher than those of Diesel. ROI profiles from the model are used as an input in CFD simulation to predict spray penetration, which are compared with spray images of both fuels captured in a combustion vessel thus providing a useful validation process for the CFD model.