Alumina as a substrate is being explored in the upcoming 5th generation radio-frequency micro-electro-mechanical system (MEMS) applications due to its superior electrical insulation, excellent wear resistance, and higher thermal conductivity. However, due to its brittle nature, its micromachining capabilities by the conventional contact-based processes has remained a challenge. This work reports the fabrication of deep micro-holes in hard-to-machine alumina substrates by the electrochemical discharge machining process. The effects of machining voltage and tool feed rate on the geometrical characteristics such as depth, overcut, sidewall profile of the micro-holes along with tool wear are reported. A high carbon steel needle having a tip size of 150 µm was used as a tool electrode, and 30wt% aqueous sodium hydroxide (NaOH) was used as an electrolyte. The experimental results reveal the optimal machining performance in terms of higher depth of micro-hole, lower overcut, and minimum tool consumption at a machining voltage of 50 V and a feed rate of 0.25 µm/s. A deep micro-holes (>300 µm) were achieved at a machining voltage of 55 V using a combined feed mechanism. The experimental results were compared to the numeric results obtained by using the finite-element method. The experimental results confirmed that machining of alumina is more difficult than glass-based materials and requires higher machining voltage; however, higher tool wear takes place at higher voltage, which in turn requires the usage of tool electrodes having a higher melting point. The research outcome of this work can be used in ceramic micromachining.