The study was performed to determine the optimum flushing condition for electrical discharge machining (EDM) of functional material titanium VT6 obtained by plasma cladding with a thermal cycle. Copper is used as an electrode tool (ET) to machine functional materials. The optimum flushing flows are analyzed theoretically by using ANSYS CFX 20.1 software which is also validated by an experimental study. It was observed that while machining the functional materials to adepth of 10 mm or more, the turbulence fluid flow dominates when nozzle angles are 45° and 75°, consequently drastically affecting the quality of flushing and the performance of the EDM. For the highest machining performance, the nozzles should be at an angle of 15° relative to the tool axis. The optimum flushing at deep hole EDM process minimizes the occurrence of debris deposition on tool electrodes, thus facilitating stable machining of functional materials. The adequacy of the obtained models was confirmed experimentally. It has been established that EDM of a hole with a depth of 15 mm, an intense accumulation of sludge, is observed in the processing zone. There arebuild-ups exceeding 3 mm in cross-section after EDM. This build-up leads to a short circuit and a reduction in surface quality and productivity. It has been proven that not correct flushing leads to intensive wear of the tool and a change in its geometric shape and, accordingly, to a decrease in the quality of EDM.